Variant rs674696 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 0.432 in 152,220 control chromosomes in the GnomAD database, including 15,716 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 0.43 ( 15716 hom., cov: 35)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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:

0.432

AC:

65747

AN:

152102

Hom.:

15698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.411

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

GnomAD4 genome

AF:

0.432

AC:

65815

AN:

152220

Hom.:

15716

Cov.:

AF XY:

0.438

AC XY:

32585

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.611

Gnomad4 AMR

AF:

0.449

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.710

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.409

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.413

Alfa

AF:

0.224

Hom.:

502

Bravo

AF:

0.446

Asia WGS

AF:

0.539

AC:

1873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.45

DANN

Benign

0.47

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