rs886774

Variant names:

• chr7-107854989-G-A
• rs886774

Your query was ambiguous. Multiple possible variants found:

• chr7-107854989-G-A
• chr7-107854989-G-C
• chr7-107854989-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.67 in 151,992 control chromosomes in the GnomAD database, including 34,902 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 0.67 (34902 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.670 AC: 101784 AN: 151874 Hom.: 34848 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.670 AC: 101899 AN: 151992 Hom.: 34902 Cov.: 31 AF XY: 0.672 AC XY: 49924 AN XY: 74288

African (AFR) AF: 0.805 AC: 33363 AN: 41456

American (AMR) AF: 0.653 AC: 9971 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2188 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4084 AN: 5168

South Asian (SAS) AF: 0.550 AC: 2646 AN: 4814

European-Finnish (FIN) AF: 0.622 AC: 6559 AN: 10548

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40856 AN: 67948

Other (OTH) AF: 0.673 AC: 1420 AN: 2110

Alfa AF: 0.623 Hom.: 87164

Bravo AF: 0.678

Asia WGS AF: 0.723 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.3
DANN	Benign	0.69
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs886774; hg19: chr7-107495434; COSMIC: COSV107155379;