Variant 15-23441399-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6

The NM_001304388.2(GOLGA6L2):c.1076A>G(p.Glu359Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 36)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L2
NM_001304388.2 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.936

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 -3 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.15146711).

BP6

Variant 15-23441399-T-C is Benign according to our data. Variant chr15-23441399-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2681302.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA6L2	NM_001304388.2 linkuse as main transcript	c.1076A>G	p.Glu359Gly	missense_variant	8/8	ENST00000567107.6	NP_001291317.1	Q8N9W4-3
GOLGA6L2	XM_047432396.1 linkuse as main transcript	c.917A>G	p.Glu306Gly	missense_variant	6/6		XP_047288352.1
GOLGA6L2	XM_047432397.1 linkuse as main transcript	c.1076A>G	p.Glu359Gly	missense_variant	8/11		XP_047288353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GOLGA6L2	ENST00000567107.6 linkuse as main transcript	c.1076A>G	p.Glu359Gly	missense_variant	8/8	5	NM_001304388.2	ENSP00000454407.1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	n.*357A>G		non_coding_transcript_exon_variant	7/7	5		ENSP00000456523.1	H3BS38
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	n.*357A>G		3_prime_UTR_variant	7/7	5		ENSP00000456523.1	H3BS38

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

149568

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1383290

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

682562

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

149568

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

73002

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00126

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma

Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.092

BayesDel_noAF

Benign

-0.37

CADD

Benign

5.1

DANN

Benign

0.83

DEOGEN2

Benign

0.014

T;T

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.00041

LIST_S2

Benign

0.038

T;T

M_CAP

Benign

0.0081

MetaRNN

Benign

0.15

T;T

MetaSVM

Benign

-0.97

MutationAssessor

Uncertain

2.6

M;.

PrimateAI

Uncertain

0.49

PROVEAN

Uncertain

-3.2

D;D

REVEL

Benign

0.029

Sift

Benign

0.044

.;D

Sift4G

Uncertain

0.0050

D;D

Polyphen

0.77

P;.

Vest4

0.068

MutPred

0.26

Loss of helix (P = 0.0041);.;

MVP

0.46

MPC

0.047

ClinPred

0.46

Varity_R

0.21

gMVP

0.67

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