rs2692877

Variant names:

• chr7-109701895-G-A
• rs2692877

Your query was ambiguous. Multiple possible variants found:

• chr7-109701895-G-A
• chr7-109701895-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;