rs10487383

Variant names:

• chr7-118031684-A-T
• rs10487383

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 0.104 in 152,192 control chromosomes in the GnomAD database, including 2,049 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 0.10 (2049 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.104 AC: 15740 AN: 152074 Hom.: 2047 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.104 AC: 15763 AN: 152192 Hom.: 2049 Cov.: 33 AF XY: 0.103 AC XY: 7637 AN XY: 74396

African (AFR) AF: 0.276 AC: 11442 AN: 41496

American (AMR) AF: 0.0653 AC: 998 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1911 AN: 5154

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4826

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10618

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0107 AC: 725 AN: 68018

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0601 Hom.: 122

Bravo AF: 0.118

Asia WGS AF: 0.205 AC: 710 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs10487383; hg19: chr7-117671738;