Variant rs275358 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 0.569 in 151,882 control chromosomes in the GnomAD database, including 25,374 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 0.57 ( 25374 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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:

0.569

AC:

86423

AN:

151764

Hom.:

25343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.672

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.766

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.720

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.692

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.604

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

GnomAD4 genome

AF:

0.569

AC:

86490

AN:

151882

Hom.:

25374

Cov.:

AF XY:

0.572

AC XY:

42484

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.446

Gnomad4 AMR

AF:

0.606

Gnomad4 ASJ

AF:

0.766

Gnomad4 EAS

AF:

0.371

Gnomad4 SAS

AF:

0.721

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.623

Gnomad4 OTH

AF:

0.605

Alfa

AF:

0.602

Hom.:

13537

Bravo

AF:

0.557

Asia WGS

AF:

0.566

AC:

1965

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.6

DANN

Benign

0.45

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