Variant rs7126715 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 0.369 in 151,786 control chromosomes in the GnomAD database, including 11,868 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 0.37 ( 11868 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.343

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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:

0.368

AC:

55881

AN:

151668

Hom.:

11844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.821

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.378

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

GnomAD4 genome

AF:

0.369

AC:

55958

AN:

151786

Hom.:

11868

Cov.:

AF XY:

0.373

AC XY:

27633

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.443

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.482

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.383

Alfa

AF:

0.281

Hom.:

8317

Bravo

AF:

0.389

Asia WGS

AF:

0.638

AC:

2211

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.72

DANN

Benign

0.52

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