Variant rs347245 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 0.515 in 152,124 control chromosomes in the GnomAD database, including 22,535 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 0.52 ( 22535 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.538

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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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:

0.516

AC:

78401

AN:

152006

Hom.:

22535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.698

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.689

Gnomad EAS

AF:

0.469

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.519

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.545

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

GnomAD4 genome

AF:

0.515

AC:

78415

AN:

152124

Hom.:

22535

Cov.:

AF XY:

0.518

AC XY:

38497

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.639

Gnomad4 ASJ

AF:

0.689

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.743

Gnomad4 FIN

AF:

0.519

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.621

Hom.:

59061

Bravo

AF:

0.511

Asia WGS

AF:

0.592

AC:

2060

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.5

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