Variant chr15-23440500-C-T 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.1975G>A(p.Glu659Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 0)

Exomes 𝑓: 0.015 ( 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: 0.432

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=0.0054126084).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
GOLGA6L2	NM_001304388.2 linkuse as main transcript	c.1975G>A	p.Glu659Lys	missense_variant	8/8	ENST00000567107.6
GOLGA6L2	XM_047432396.1 linkuse as main transcript	c.1816G>A	p.Glu606Lys	missense_variant	6/6
GOLGA6L2	XM_047432397.1 linkuse as main transcript	c.1254G>A	p.Glu418=	synonymous_variant	10/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L2	ENST00000567107.6 linkuse as main transcript	c.1975G>A	p.Glu659Lys	missense_variant	8/8	5	NM_001304388.2	P1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	c.*1256G>A		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

13778

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000841

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.0229

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000768

Gnomad OTH

AF:

0.00758

GnomAD3 exomes

AF:

0.000580

AC:

AN:

25850

Hom.:

AF XY:

0.000382

AC XY:

AN XY:

13082

show subpopulations

Gnomad AFR exome

AF:

0.00157

Gnomad AMR exome

AF:

0.000509

Gnomad ASJ exome

AF:

0.00111

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00196

Gnomad NFE exome

AF:

0.000411

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0150

AC:

1797

AN:

120004

Hom.:

Cov.:

AF XY:

0.0140

AC XY:

861

AN XY:

61710

show subpopulations

Gnomad4 AFR exome

AF:

0.00397

Gnomad4 AMR exome

AF:

0.00134

Gnomad4 ASJ exome

AF:

0.00779

Gnomad4 EAS exome

AF:

0.00206

Gnomad4 SAS exome

AF:

0.00405

Gnomad4 FIN exome

AF:

0.00163

Gnomad4 NFE exome

AF:

0.0198

Gnomad4 OTH exome

AF:

0.0116

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00116

AC:

AN:

13804

Hom.:

Cov.:

AF XY:

0.000891

AC XY:

AN XY:

6732

show subpopulations

Gnomad4 AFR

AF:

0.000837

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.0229

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000768

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.415

Hom.:

ExAC

AF:

0.0000819

AC:

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

0.31

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.89

FATHMM_MKL

Benign

0.00095

LIST_S2

Benign

0.64

M_CAP

Benign

0.0027

MetaRNN

Benign

0.0054

MutationTaster

Benign

1.0

P;P;P

PROVEAN

Benign

-0.32

Sift4G

Benign

0.33

Vest4

0.14

MVP

0.030

MPC

0.014

Varity_R

0.20

gMVP

0.065

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