Variant rs16862537 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 0.2 in 151,962 control chromosomes in the GnomAD database, including 3,782 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 0.20 ( 3782 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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:

0.201

AC:

30453

AN:

151842

Hom.:

3785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0586

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.357

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.271

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.230

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

GnomAD4 genome

AF:

0.200

AC:

30438

AN:

151962

Hom.:

3782

Cov.:

AF XY:

0.197

AC XY:

14613

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.0585

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.357

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.276

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.206

Hom.:

546

Bravo

AF:

0.196

Asia WGS

AF:

0.206

AC:

719

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.74

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