rs121909352

Positions:

chr8-96145185-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

The NM_001001557.4(GDF6):c.746C>A(p.Ala249Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00367 in 1,496,680 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0039 ( 15 hom. )

Consequence

GDF6
NM_001001557.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5U:4B:4

Conservation

PhyloP100: 0.269

Variant links:

Genes affected

GDF6 (HGNC:4221): (growth differentiation factor 6) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein is required for normal formation of some bones and joints in the limbs, skull, and axial skeleton. Mutations in this gene are associated with Klippel-Feil syndrome, microphthalmia, and Leber congenital amaurosis. [provided by RefSeq, Sep 2016]

GDF6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.036596745).

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00386 (5191/1344460) while in subpopulation NFE AF= 0.00464 (4926/1062610). AF 95% confidence interval is 0.00453. There are 15 homozygotes in gnomad4_exome. There are 2492 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAdExome4 at 15 AD,AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GDF6	NM_001001557.4 linkuse as main transcript	c.746C>A	p.Ala249Glu	missense_variant	2/2	ENST00000287020.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GDF6	ENST00000287020.7 linkuse as main transcript	c.746C>A	p.Ala249Glu	missense_variant	2/2	1	NM_001001557.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00197

AC:

299

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000676

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00353

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00198

AC:

192

AN:

97088

Hom.:

AF XY:

0.00216

AC XY:

118

AN XY:

54644

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00203

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000384

Gnomad NFE exome

AF:

0.00401

Gnomad OTH exome

AF:

0.00172

GnomAD4 exome

AF:

0.00386

AC:

5191

AN:

1344460

Hom.:

Cov.:

AF XY:

0.00376

AC XY:

2492

AN XY:

662802

show subpopulations

Gnomad4 AFR exome

AF:

0.000767

Gnomad4 AMR exome

AF:

0.00191

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000267

Gnomad4 FIN exome

AF:

0.000245

Gnomad4 NFE exome

AF:

0.00464

Gnomad4 OTH exome

AF:

0.00311

GnomAD4 genome

AF:

0.00196

AC:

298

AN:

152220

Hom.:

Cov.:

AF XY:

0.00173

AC XY:

129

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.000650

Gnomad4 AMR

AF:

0.00176

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00353

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00226

Hom.:

Bravo

AF:

0.00215

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00259

AC:

ExAC

AF:

0.000992

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5Uncertain:4Benign:4

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:2Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 18, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	GDF6: BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2019	Does not segregate with Chiari Malformation type 1 in all affected individuals in published literature (Markunas et al., 2013); Published functional studies suggest this variant results in a decrease of activity as compared to wild-type (Asai-Coakwell et al., 2013); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 20494911, 29343940, 23620759, 18425797, 19129173, 21864080, 25457163, 23307924, 31068177, 29260090, 30755392, 32737436) -

Klippel-Feil syndrome 1, autosomal dominant

Pathogenic:1Uncertain:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 2013	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Aug 13, 2019	- -

Isolated microphthalmia 4

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 01, 2013

- -

Congenital anomaly of kidney and urinary tract

Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Weber Lab, Hannover Medical School

Feb 15, 2024

- -

Klippel-Feil syndrome 1, autosomal dominant;C1968949:Congenital anomaly of kidney and urinary tract

Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Weber Lab, Hannover Medical School

Feb 15, 2024

- -

Leber congenital amaurosis 17

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 01, 2013

- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: low reads, pathogenic by OMIM in ClinVar, implicated in different pathologies -

GDF6-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 28, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Klippel-Feil syndrome 1, autosomal dominant;C2751307:Isolated microphthalmia 4;C3150968:Microphthalmia, isolated, with coloboma 6;C3715164:Leber congenital amaurosis 17

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 18, 2024

- -

Klippel-Feil syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.30

CADD

Benign

5.9

DANN

Benign

0.92

DEOGEN2

Benign

0.38

T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.076

LIST_S2

Benign

0.36

T;T

M_CAP

Uncertain

0.18

MetaRNN

Benign

0.037

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.92

L;.

MutationTaster

Benign

5.2e-12

PrimateAI

Pathogenic

0.79

PROVEAN

Benign

-0.92

N;.

REVEL

Benign

0.27

Sift

Benign

0.093

T;.

Sift4G

Benign

0.59

T;D

Polyphen

0.012

B;.

Vest4

0.10

MVP

0.97

MPC

0.94

ClinPred

0.013

GERP RS

0.81

Varity_R

0.065

gMVP

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over