Variant rs10239907 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 0.219 in 151,570 control chromosomes in the GnomAD database, including 3,769 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 0.22 ( 3769 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.113

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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:

0.219

AC:

33125

AN:

151466

Hom.:

3766

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.219

AC:

33141

AN:

151570

Hom.:

3769

Cov.:

AF XY:

0.222

AC XY:

16440

AN XY:

74044

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.213

Alfa

AF:

0.229

Hom.:

6978

Bravo

AF:

0.214

Asia WGS

AF:

0.228

AC:

794

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.2

DANN

Benign

0.76

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