Variant rs714597 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 0.327 in 108,430 control chromosomes in the GnomAD database, including 4,476 homozygotes. There are 9,963 hemizygotes in GnomAD. 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 0.33 ( 4476 hom., 9963 hem., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.687

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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:

0.327

AC:

35430

AN:

108382

Hom.:

4474

Cov.:

AF XY:

0.323

AC XY:

9948

AN XY:

30790

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.387

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.325

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

GnomAD4 genome

AF:

0.327

AC:

35443

AN:

108430

Hom.:

4476

Cov.:

AF XY:

0.323

AC XY:

9963

AN XY:

30848

show subpopulations

Gnomad4 AFR

AF:

0.321

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.552

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.140

Hom.:

661

Bravo

AF:

0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.5

DANN

Benign

0.61

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