Variant rs908857 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 0.608 in 152,314 control chromosomes in the GnomAD database, including 29,757 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 0.61 ( 29687 hom., cov: 30)

Exomes 𝑓: 0.58 ( 70 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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:

0.607

AC:

92177

AN:

151762

Hom.:

29643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.836

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.488

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.573

GnomAD4 exome

AF:

0.581

AC:

252

AN:

434

Hom.:

AF XY:

0.580

AC XY:

152

AN XY:

262

show subpopulations

Gnomad4 FIN exome

AF:

0.575

Gnomad4 NFE exome

AF:

0.750

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.608

AC:

92279

AN:

151880

Hom.:

29687

Cov.:

AF XY:

0.604

AC XY:

44824

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.836

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.511

Gnomad4 EAS

AF:

0.488

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.562

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.525

Hom.:

35282

Bravo

AF:

0.620

Asia WGS

AF:

0.479

AC:

1667

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.18

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