Variant rs5975493 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 0.415 in 109,066 control chromosomes in the GnomAD database, including 7,163 homozygotes. There are 12,393 hemizygotes in GnomAD. 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 0.42 ( 7163 hom., 12393 hem., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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:

0.416

AC:

45302

AN:

109018

Hom.:

7166

Cov.:

AF XY:

0.395

AC XY:

12374

AN XY:

31356

show subpopulations

Gnomad AFR

AF:

0.398

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.418

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

GnomAD4 genome

AF:

0.415

AC:

45313

AN:

109066

Hom.:

7163

Cov.:

AF XY:

0.395

AC XY:

12393

AN XY:

31414

show subpopulations

Gnomad4 AFR

AF:

0.397

Gnomad4 AMR

AF:

0.394

Gnomad4 ASJ

AF:

0.438

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.387

Gnomad4 NFE

AF:

0.458

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.244

Hom.:

1092

Bravo

AF:

0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.4

DANN

Benign

0.87

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