Variant rs997161 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 0.757 in 152,010 control chromosomes in the GnomAD database, including 43,680 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 0.76 ( 43680 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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:

0.757

AC:

114980

AN:

151892

Hom.:

43655

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

0.861

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.772

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.748

Gnomad OTH

AF:

0.769

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

GnomAD4 genome

AF:

0.757

AC:

115053

AN:

152010

Hom.:

43680

Cov.:

AF XY:

0.754

AC XY:

56062

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.783

Gnomad4 AMR

AF:

0.761

Gnomad4 ASJ

AF:

0.772

Gnomad4 EAS

AF:

0.834

Gnomad4 SAS

AF:

0.713

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.748

Gnomad4 OTH

AF:

0.768

Alfa

AF:

0.754

Hom.:

72566

Bravo

AF:

0.763

Asia WGS

AF:

0.751

AC:

2613

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.88

DANN

Benign

0.19

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