Variant rs2346747 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 0.544 in 152,046 control chromosomes in the GnomAD database, including 25,003 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 0.54 ( 25003 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.210

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=-0.73).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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:

0.544

AC:

82640

AN:

151928

Hom.:

25002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.685

Gnomad EAS

AF:

0.579

Gnomad SAS

AF:

0.594

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.666

Gnomad OTH

AF:

0.588

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

GnomAD4 genome

AF:

0.544

AC:

82661

AN:

152046

Hom.:

25003

Cov.:

AF XY:

0.546

AC XY:

40595

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.254

Gnomad4 AMR

AF:

0.649

Gnomad4 ASJ

AF:

0.685

Gnomad4 EAS

AF:

0.579

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.645

Gnomad4 NFE

AF:

0.666

Gnomad4 OTH

AF:

0.583

Alfa

AF:

0.450

Hom.:

1347

Bravo

AF:

0.532

Asia WGS

AF:

0.534

AC:

1862

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.3

DANN

Benign

0.70

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