Variant rs1472343 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 0.443 in 151,886 control chromosomes in the GnomAD database, including 15,195 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 0.44 ( 15195 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.280

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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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:

0.443

AC:

67187

AN:

151770

Hom.:

15154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.501

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.452

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.432

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

GnomAD4 genome

AF:

0.443

AC:

67280

AN:

151886

Hom.:

15195

Cov.:

AF XY:

0.441

AC XY:

32739

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.477

Gnomad4 ASJ

AF:

0.503

Gnomad4 EAS

AF:

0.501

Gnomad4 SAS

AF:

0.513

Gnomad4 FIN

AF:

0.338

Gnomad4 NFE

AF:

0.416

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.262

Hom.:

570

Bravo

AF:

0.455

Asia WGS

AF:

0.551

AC:

1913

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.063

DANN

Benign

0.79

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