Variant 15-22465656-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001396956.1(GOLGA6L22):c.1396G>T(p.Glu466Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 6)

Exomes 𝑓: 0.0021 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L22
NM_001396956.1 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.82

Variant links:

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

GOLGA6L22 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 15-22465656-G-T is Benign according to our data. Variant chr15-22465656-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644965.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA6L22	NM_001396956.1 linkuse as main transcript	c.1396G>T	p.Glu466Ter	stop_gained	8/9	ENST00000622895.2
GOLGA6L22	NM_001396957.1 linkuse as main transcript	c.1393G>T	p.Glu465Ter	stop_gained	8/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L22	ENST00000622895.2 linkuse as main transcript	c.1396G>T	p.Glu466Ter	stop_gained	8/9	5	NM_001396956.1	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

36828

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000163

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:

0.000228

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000651

AC:

AN:

153556

Hom.:

AF XY:

0.00

AC XY:

AN XY:

81230

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000440

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:

0.00214

AC:

1688

AN:

788654

Hom.:

Cov.:

AF XY:

0.00228

AC XY:

922

AN XY:

403688

show subpopulations

Gnomad4 AFR exome

AF:

0.00325

Gnomad4 AMR exome

AF:

0.00212

Gnomad4 ASJ exome

AF:

0.00500

Gnomad4 EAS exome

AF:

0.000193

Gnomad4 SAS exome

AF:

0.00537

Gnomad4 FIN exome

AF:

0.00113

Gnomad4 NFE exome

AF:

0.00181

Gnomad4 OTH exome

AF:

0.00285

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000163

AC:

AN:

36852

Hom.:

Cov.:

AF XY:

0.000172

AC XY:

AN XY:

17424

show subpopulations

Gnomad4 AFR

AF:

0.000162

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:

0.000228

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00320

Hom.:

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

Jan 01, 2023

RP11-467N20.5: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.25

BayesDel_noAF

Uncertain

0.12

CADD

Benign

DANN

Benign

0.97

Eigen

Uncertain

0.27

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.0035

MutationTaster

Benign

1.0

A;A;N

Vest4

0.043

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