Variant rs13134954 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 0.332 in 151,950 control chromosomes in the GnomAD database, including 8,606 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 0.33 ( 8606 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50416

AN:

151832

Hom.:

8587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.373

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

GnomAD4 genome

AF:

0.332

AC:

50482

AN:

151950

Hom.:

8606

Cov.:

AF XY:

0.328

AC XY:

24337

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.387

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.393

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.361

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.354

Hom.:

7413

Bravo

AF:

0.342

Asia WGS

AF:

0.294

AC:

1022

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.0

DANN

Benign

0.41

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