Variant rs17622933 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 0.264 in 151,914 control chromosomes in the GnomAD database, including 6,063 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 0.26 ( 6063 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461

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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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:

0.264

AC:

40065

AN:

151796

Hom.:

6058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.555

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.264

AC:

40085

AN:

151914

Hom.:

6063

Cov.:

AF XY:

0.263

AC XY:

19534

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.274

Gnomad4 ASJ

AF:

0.353

Gnomad4 EAS

AF:

0.555

Gnomad4 SAS

AF:

0.419

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.144

Hom.:

287

Bravo

AF:

0.264

Asia WGS

AF:

0.437

AC:

1516

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.1

DANN

Benign

0.72

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