Variant 13-37616450-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.294 in 152,008 control chromosomes in the GnomAD database, including 6,992 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 6992 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.510

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44638

AN:

151890

Hom.:

6982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.294

AC:

44665

AN:

152008

Hom.:

6992

Cov.:

AF XY:

0.285

AC XY:

21184

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.161

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.351

Gnomad4 OTH

AF:

0.312

Alfa

AF:

0.324

Hom.:

1039

Bravo

AF:

0.294

Asia WGS

AF:

0.257

AC:

894

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.88

DANN

Benign

0.73

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over