Variant 15-23440127-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001304388.2(GOLGA6L2):c.2348T>C(p.Val783Ala) 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0026 ( 131 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L2
NM_001304388.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0290

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 -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0052158833).

BP6

Variant 15-23440127-A-G is Benign according to our data. Variant chr15-23440127-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2644971.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA6L2	NM_001304388.2 linkuse as main transcript	c.2348T>C	p.Val783Ala	missense_variant	8/8	ENST00000567107.6	NP_001291317.1	Q8N9W4-3
GOLGA6L2	XM_047432396.1 linkuse as main transcript	c.2189T>C	p.Val730Ala	missense_variant	6/6		XP_047288352.1
GOLGA6L2	XM_047432397.1 linkuse as main transcript	c.1444T>C	p.Trp482Arg	missense_variant	11/11		XP_047288353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GOLGA6L2	ENST00000567107.6 linkuse as main transcript	c.2348T>C	p.Val783Ala	missense_variant	8/8	5	NM_001304388.2	ENSP00000454407.1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	n.*1629T>C		non_coding_transcript_exon_variant	7/7	5		ENSP00000456523.1	H3BS38
GOLGA6L2	ENST00000566571.5 linkuse as main transcript	n.*1629T>C		3_prime_UTR_variant	7/7	5		ENSP00000456523.1	H3BS38

Frequencies

GnomAD3 genomes

AF:

0.00179

AC:

AN:

13376

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00375

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

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

GnomAD3 exomes

AF:

0.00179

AC:

AN:

29686

Hom.:

AF XY:

0.00185

AC XY:

AN XY:

16206

show subpopulations

Gnomad AFR exome

AF:

0.0164

Gnomad AMR exome

AF:

0.00104

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000178

Gnomad FIN exome

AF:

0.000776

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00118

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00257

AC:

304

AN:

118474

Hom.:

131

Cov.:

AF XY:

0.00215

AC XY:

140

AN XY:

65050

show subpopulations

Gnomad4 AFR exome

AF:

0.0341

Gnomad4 AMR exome

AF:

0.00312

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000367

Gnomad4 NFE exome

AF:

0.000125

Gnomad4 OTH exome

AF:

0.00568

GnomAD4 genome

AF:

0.00179

AC:

AN:

13410

Hom.:

Cov.:

AF XY:

0.00184

AC XY:

AN XY:

6532

show subpopulations

Gnomad4 AFR

AF:

0.00373

Gnomad4 AMR

AF:

0.00124

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:

0.0688

Hom.:

ExAC

AF:

0.00145

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

GOLGA6L2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.0

DANN

Benign

0.27

FATHMM_MKL

Benign

0.00023

LIST_S2

Benign

0.37

M_CAP

Benign

0.0040

MetaRNN

Benign

0.0052

PROVEAN

Benign

-0.24

Sift4G

Benign

0.76

Vest4

0.17

MVP

0.030

MPC

0.014

Varity_R

0.065

gMVP

0.015

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