Variant 15-20534687-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001145004.2(GOLGA6L6):c.1747A>G(p.Lys583Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00013 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -4.81

Variant links:

Genes affected

GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

GOLGA6L6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.05003071).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA6L6	NM_001145004.2 linkuse as main transcript	c.1747A>G	p.Lys583Glu	missense_variant	8/9	ENST00000619213.1	NP_001138476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLGA6L6	ENST00000619213.1 linkuse as main transcript	c.1747A>G	p.Lys583Glu	missense_variant	8/9	5	NM_001145004.2	ENSP00000480376	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

124

AN:

50242

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00233

Gnomad AMI

AF:

0.00403

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.00336

Gnomad EAS

AF:

0.000664

Gnomad SAS

AF:

0.00205

Gnomad FIN

AF:

0.00190

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00284

Gnomad OTH

AF:

0.00289

GnomAD3 exomes

AF:

0.0000470

AC:

AN:

106366

Hom.:

AF XY:

0.0000695

AC XY:

AN XY:

57538

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000113

Gnomad ASJ exome

AF:

0.000147

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000508

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000133

AC:

108

AN:

812444

Hom.:

Cov.:

AF XY:

0.000146

AC XY:

AN XY:

390156

show subpopulations

Gnomad4 AFR exome

AF:

0.000513

Gnomad4 AMR exome

AF:

0.000665

Gnomad4 ASJ exome

AF:

0.000364

Gnomad4 EAS exome

AF:

0.000292

Gnomad4 SAS exome

AF:

0.000243

Gnomad4 FIN exome

AF:

0.000294

Gnomad4 NFE exome

AF:

0.000100

Gnomad4 OTH exome

AF:

0.0000341

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00246

AC:

124

AN:

50312

Hom.:

Cov.:

AF XY:

0.00243

AC XY:

AN XY:

25062

show subpopulations

Gnomad4 AFR

AF:

0.00232

Gnomad4 AMR

AF:

0.00184

Gnomad4 ASJ

AF:

0.00336

Gnomad4 EAS

AF:

0.000665

Gnomad4 SAS

AF:

0.00205

Gnomad4 FIN

AF:

0.00190

Gnomad4 NFE

AF:

0.00284

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.0945

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 17, 2023

The c.1825A>G (p.K609E) alteration is located in exon 8 (coding exon 8) of the GOLGA6L6 gene. This alteration results from a A to G substitution at nucleotide position 1825, causing the lysine (K) at amino acid position 609 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.13

DANN

Benign

0.31

DEOGEN2

Benign

0.00042

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0017

LIST_S2

Benign

0.18

M_CAP

Benign

0.021

MetaRNN

Benign

0.050

MetaSVM

Benign

-0.92

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.56

Sift4G

Benign

1.0

Vest4

0.049

MVP

0.014

ClinPred

0.038

Varity_R

0.072

gMVP

0.0012

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