rs2692877

chr7-109701895-G-Achr7-109701895-G-T

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 0.496 in 151,730 control chromosomes in the GnomAD database, including 18,940 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 0.50 (18940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 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: 0.495 AC: 75111 AN: 151612 Hom.: 18911 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.496 AC: 75192 AN: 151730 Hom.: 18940 Cov.: 32 AF XY: 0.498 AC XY: 36922 AN XY: 74110

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.484

Alfa AF: 0.471 Hom.: 2446

Bravo AF: 0.488

Asia WGS AF: 0.594 AC: 2063 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2692877; hg19: chr7-109341952;