Variant chr15-23440461-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_001304388.2(GOLGA6L2):c.2014A>G(p.Arg672Gly) 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 0.0047 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00081 ( 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: -1.17

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=0.0064904094).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
GOLGA6L2	NM_001304388.2 linkuse as main transcript	c.2014A>G	p.Arg672Gly	missense_variant	8/8	ENST00000567107.6
GOLGA6L2	XM_047432396.1 linkuse as main transcript	c.1855A>G	p.Arg619Gly	missense_variant	6/6
GOLGA6L2	XM_047432397.1 linkuse as main transcript	c.1293A>G	p.Glu431=	synonymous_variant	10/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L2	ENST00000567107.6 linkuse as main transcript	c.2014A>G	p.Arg672Gly	missense_variant	8/8	5	NM_001304388.2	P1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	c.*1295A>G		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

19704

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00396

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.00575

Gnomad EAS

AF:

0.00562

Gnomad SAS

AF:

0.00198

Gnomad FIN

AF:

0.000867

Gnomad MID

AF:

0.0263

Gnomad NFE

AF:

0.00694

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000810

AC:

162

AN:

199982

Hom.:

Cov.:

AF XY:

0.000885

AC XY:

AN XY:

100582

show subpopulations

Gnomad4 AFR exome

AF:

0.000948

Gnomad4 AMR exome

AF:

0.00549

Gnomad4 ASJ exome

AF:

0.00126

Gnomad4 EAS exome

AF:

0.00212

Gnomad4 SAS exome

AF:

0.00198

Gnomad4 FIN exome

AF:

0.000598

Gnomad4 NFE exome

AF:

0.000518

Gnomad4 OTH exome

AF:

0.000742

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00471

AC:

AN:

19756

Hom.:

Cov.:

AF XY:

0.00330

AC XY:

AN XY:

9696

show subpopulations

Gnomad4 AFR

AF:

0.00394

Gnomad4 AMR

AF:

0.00208

Gnomad4 ASJ

AF:

0.00575

Gnomad4 EAS

AF:

0.00562

Gnomad4 SAS

AF:

0.00198

Gnomad4 FIN

AF:

0.000867

Gnomad4 NFE

AF:

0.00694

Gnomad4 OTH

AF:

0.00391

Alfa

AF:

0.433

Hom.:

ExAC

AF:

0.0000907

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

0.059

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.5

DANN

Benign

0.52

FATHMM_MKL

Benign

0.00028

LIST_S2

Benign

0.42

M_CAP

Benign

0.0031

MetaRNN

Benign

0.0065

MutationTaster

Benign

1.0

N;N;N

PROVEAN

Benign

-0.80

Sift4G

Benign

1.0

Vest4

0.21

MVP

0.040

MPC

0.014

Varity_R

0.13

gMVP

0.041

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