Variant chr15-23440773-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_001304388.2(GOLGA6L2):c.1702T>G(p.Ser568Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0063 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000017 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L2
NM_001304388.2 missense

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.690

Variant links:

Genes affected

GOLGA6L2 (HGNC:26695): (golgin A6 family like 2) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA6L2 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=0.010241866).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
GOLGA6L2	NM_001304388.2 linkuse as main transcript	c.1702T>G	p.Ser568Ala	missense_variant	8/8	ENST00000567107.6
GOLGA6L2	XM_047432396.1 linkuse as main transcript	c.1543T>G	p.Ser515Ala	missense_variant	6/6
GOLGA6L2	XM_047432397.1 linkuse as main transcript	c.1228-247T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L2	ENST00000567107.6 linkuse as main transcript	c.1702T>G	p.Ser568Ala	missense_variant	8/8	5	NM_001304388.2	P1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	c.*983T>G		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes

AF:

0.00629

AC:

226

AN:

35938

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0102

Gnomad AMI

AF:

0.00820

Gnomad AMR

AF:

0.00187

Gnomad ASJ

AF:

0.00728

Gnomad EAS

AF:

0.0151

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.000461

Gnomad MID

AF:

0.0139

Gnomad NFE

AF:

0.00484

Gnomad OTH

AF:

0.00791

GnomAD3 exomes

AF:

0.0000676

AC:

AN:

44378

Hom.:

AF XY:

0.0000773

AC XY:

AN XY:

25874

show subpopulations

Gnomad AFR exome

AF:

0.000797

Gnomad AMR exome

AF:

0.000254

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00107

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000168

AC:

AN:

1249250

Hom.:

Cov.:

AF XY:

0.0000210

AC XY:

AN XY:

619626

show subpopulations

Gnomad4 AFR exome

AF:

0.0000722

Gnomad4 AMR exome

AF:

0.000121

Gnomad4 ASJ exome

AF:

0.0000431

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000137

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000104

Gnomad4 OTH exome

AF:

0.0000571

GnomAD4 genome

AF:

0.00628

AC:

226

AN:

35974

Hom.:

Cov.:

AF XY:

0.00525

AC XY:

AN XY:

17332

show subpopulations

Gnomad4 AFR

AF:

0.0101

Gnomad4 AMR

AF:

0.00214

Gnomad4 ASJ

AF:

0.00728

Gnomad4 EAS

AF:

0.0151

Gnomad4 SAS

AF:

0.00478

Gnomad4 FIN

AF:

0.000461

Gnomad4 NFE

AF:

0.00484

Gnomad4 OTH

AF:

0.00586

Alfa

AF:

0.315

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.46

CADD

Benign

1.7

DANN

Benign

0.71

FATHMM_MKL

Benign

0.00025

LIST_S2

Benign

0.16

M_CAP

Benign

0.017

MetaRNN

Benign

0.010

MutationTaster

Benign

1.0

N;N;N

PROVEAN

Benign

-0.010

Sift4G

Benign

1.0

Vest4

0.13

MVP

0.35

MPC

0.013

Varity_R

0.099

gMVP

0.014

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