rs2693737

chr7-129791154-G-Achr7-129791154-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.911 in 152,232 control chromosomes in the GnomAD database, including 63,320 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 0.91 (63320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 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: 0.911 AC: 138647 AN: 152114 Hom.: 63267 Cov.: 31

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.911 AC: 138757 AN: 152232 Hom.: 63320 Cov.: 31 AF XY: 0.914 AC XY: 67979 AN XY: 74404

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.917

Alfa AF: 0.914 Hom.: 92668

Bravo AF: 0.913

Asia WGS AF: 0.971 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.0070
Dann	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2693737; hg19: chr7-129430994;