Variant chr1-43063532-C-T 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 0.467 in 152,104 control chromosomes in the GnomAD database, including 19,896 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 0.47 ( 19896 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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:

0.467

AC:

70978

AN:

151986

Hom.:

19897

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.500

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

GnomAD4 genome

AF:

0.467

AC:

70979

AN:

152104

Hom.:

19896

Cov.:

AF XY:

0.466

AC XY:

34625

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.520

Gnomad4 FIN

AF:

0.575

Gnomad4 NFE

AF:

0.629

Gnomad4 OTH

AF:

0.503

Alfa

AF:

0.503

Hom.:

3692

Bravo

AF:

0.446

Asia WGS

AF:

0.463

AC:

1607

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.6

DANN

Benign

0.66

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