Variant rs10399805 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 0.176 in 574,560 control chromosomes in the GnomAD database, including 11,758 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 ( 4964 hom., cov: 32)

Exomes 𝑓: 0.16 ( 6794 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.532

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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:

0.222

AC:

33798

AN:

151928

Hom.:

4944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.0689

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.222

GnomAD4 exome

AF:

0.159

AC:

67083

AN:

422512

Hom.:

6794

AF XY:

0.157

AC XY:

34740

AN XY:

221602

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.328

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.314

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.0723

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.222

AC:

33830

AN:

152048

Hom.:

4964

Cov.:

AF XY:

0.222

AC XY:

16490

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.389

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.191

Gnomad4 EAS

AF:

0.279

Gnomad4 SAS

AF:

0.145

Gnomad4 FIN

AF:

0.0689

Gnomad4 NFE

AF:

0.127

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.0463

Hom.:

Bravo

AF:

0.253

Asia WGS

AF:

0.219

AC:

759

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.7

DANN

Benign

0.64

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