Variant 15-20534396-A-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.2038T>G(p.Trp680Gly) 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 not provided (no stars).

Frequency

Genomes: 𝑓 0.11 ( 0 hom., cov: 7)

Exomes 𝑓: 0.023 ( 10 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -5.44

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=0.006571591).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L6	NM_001145004.2 link	c.2038T>G	p.Trp680Gly	missense_variant	Exon 8 of 9	ENST00000619213.1	NP_001138476.2	A8MZA4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L6	ENST00000619213.1 link	c.2038T>G	p.Trp680Gly	missense_variant	Exon 8 of 9	5	NM_001145004.2	ENSP00000480376.1		A8MZA4

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

5484

AN:

50982

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.0995

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0372

Gnomad SAS

AF:

0.0933

Gnomad FIN

AF:

0.0812

Gnomad MID

AF:

0.100

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.0909

GnomAD3 exomes

AF:

0.00383

AC:

429

AN:

111990

Hom.:

AF XY:

0.00343

AC XY:

210

AN XY:

61186

show subpopulations

Gnomad AFR exome

AF:

0.00777

Gnomad AMR exome

AF:

0.00499

Gnomad ASJ exome

AF:

0.000929

Gnomad EAS exome

AF:

0.00575

Gnomad SAS exome

AF:

0.00280

Gnomad FIN exome

AF:

0.000165

Gnomad NFE exome

AF:

0.00404

Gnomad OTH exome

AF:

0.00387

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0233

AC:

18019

AN:

774024

Hom.:

Cov.:

AF XY:

0.0225

AC XY:

8748

AN XY:

389626

show subpopulations

Gnomad4 AFR exome

AF:

0.0331

Gnomad4 AMR exome

AF:

0.0156

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.00438

Gnomad4 SAS exome

AF:

0.0238

Gnomad4 FIN exome

AF:

0.00675

Gnomad4 NFE exome

AF:

0.0255

Gnomad4 OTH exome

AF:

0.0221

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.108

AC:

5487

AN:

51038

Hom.:

Cov.:

AF XY:

0.102

AC XY:

2534

AN XY:

24848

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.0992

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.0374

Gnomad4 SAS

AF:

0.0963

Gnomad4 FIN

AF:

0.0812

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.0892

Alfa

AF:

0.00835

Hom.:

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.029

DANN

Benign

0.29

DEOGEN2

Benign

0.0025

Eigen

Benign

-2.3

Eigen_PC

Benign

-2.4

FATHMM_MKL

Benign

0.00042

LIST_S2

Benign

0.056

M_CAP

Benign

0.0033

MetaRNN

Benign

0.0066

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.53

Sift4G

Benign

0.69

Vest4

0.099

MVP

0.030

ClinPred

0.0020

Varity_R

0.065

gMVP

0.0035

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