Variant rs4958849 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 0.74 in 152,002 control chromosomes in the GnomAD database, including 43,611 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 0.74 ( 43611 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 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:

0.740

AC:

112407

AN:

151884

Hom.:

43616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.491

Gnomad AMI

AF:

0.875

Gnomad AMR

AF:

0.709

Gnomad ASJ

AF:

0.814

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.791

Gnomad FIN

AF:

0.850

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.873

Gnomad OTH

AF:

0.751

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

GnomAD4 genome

AF:

0.740

AC:

112436

AN:

152002

Hom.:

43611

Cov.:

AF XY:

0.738

AC XY:

54830

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.490

Gnomad4 AMR

AF:

0.708

Gnomad4 ASJ

AF:

0.814

Gnomad4 EAS

AF:

0.724

Gnomad4 SAS

AF:

0.791

Gnomad4 FIN

AF:

0.850

Gnomad4 NFE

AF:

0.873

Gnomad4 OTH

AF:

0.751

Alfa

AF:

0.805

Hom.:

8298

Bravo

AF:

0.716

Asia WGS

AF:

0.735

AC:

2555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.5

DANN

Benign

0.79

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