Variant rs9965170 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 0.371 in 148,758 control chromosomes in the GnomAD database, including 10,817 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 0.37 ( 10817 hom., cov: 27)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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:

0.371

AC:

55118

AN:

148688

Hom.:

10814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.467

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.385

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

GnomAD4 genome

AF:

0.371

AC:

55117

AN:

148758

Hom.:

10817

Cov.:

AF XY:

0.372

AC XY:

26911

AN XY:

72330

show subpopulations

Gnomad4 AFR

AF:

0.248

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.434

Gnomad4 FIN

AF:

0.473

Gnomad4 NFE

AF:

0.428

Gnomad4 OTH

AF:

0.384

Alfa

AF:

0.297

Hom.:

1144

Bravo

AF:

0.357

Asia WGS

AF:

0.263

AC:

917

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.037

DANN

Benign

0.80

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