Variant rs1611192 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 0.197 in 288,962 control chromosomes in the GnomAD database, including 6,179 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 ( 3634 hom., cov: 32)

Exomes 𝑓: 0.18 ( 2545 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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:

0.217

AC:

32953

AN:

152056

Hom.:

3635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.183

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.0675

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.219

GnomAD4 exome

AF:

0.176

AC:

24032

AN:

136788

Hom.:

2545

AF XY:

0.179

AC XY:

12807

AN XY:

71608

show subpopulations

Gnomad4 AFR exome

AF:

0.197

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.0521

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.144

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.217

AC:

32950

AN:

152174

Hom.:

3634

Cov.:

AF XY:

0.211

AC XY:

15715

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.216

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.0676

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.238

Hom.:

3295

Bravo

AF:

0.222

Asia WGS

AF:

0.132

AC:

463

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.0

DANN

Benign

0.52

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