Variant rs1432982 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 0.49 in 152,026 control chromosomes in the GnomAD database, including 21,210 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 0.49 ( 21210 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

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 (AFR) allele frequency at 95% confidence interval = 0.776 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:

0.490

AC:

74424

AN:

151908

Hom.:

21164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.686

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.476

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

GnomAD4 genome

AF:

0.490

AC:

74532

AN:

152026

Hom.:

21210

Cov.:

AF XY:

0.486

AC XY:

36088

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.783

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.490

Gnomad4 EAS

AF:

0.686

Gnomad4 SAS

AF:

0.469

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.479

Alfa

AF:

0.397

Hom.:

2528

Bravo

AF:

0.514

Asia WGS

AF:

0.615

AC:

2136

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

3.0

DANN

Benign

0.56

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