Variant rs607375 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 0.637 in 152,324 control chromosomes in the GnomAD database, including 31,544 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 0.64 ( 31489 hom., cov: 33)

Exomes 𝑓: 0.66 ( 55 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.310

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 (SAS) allele frequency at 95% confidence interval = 0.694 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:

0.637

AC:

96737

AN:

151964

Hom.:

31467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.825

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.676

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.709

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.658

GnomAD4 exome

AF:

0.661

AC:

160

AN:

242

Hom.:

AF XY:

0.651

AC XY:

AN XY:

146

show subpopulations

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.659

Gnomad4 NFE exome

AF:

0.800

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.637

AC:

96804

AN:

152082

Hom.:

31489

Cov.:

AF XY:

0.634

AC XY:

47181

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.495

Gnomad4 AMR

AF:

0.686

Gnomad4 ASJ

AF:

0.676

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.710

Gnomad4 FIN

AF:

0.685

Gnomad4 NFE

AF:

0.699

Gnomad4 OTH

AF:

0.660

Alfa

AF:

0.671

Hom.:

4317

Bravo

AF:

0.630

Asia WGS

AF:

0.653

AC:

2269

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

DANN

Benign

0.57

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