rs10487799

Variant names:

• chr7-15058106-G-A
• rs10487799

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 0.158 in 151,994 control chromosomes in the GnomAD database, including 2,101 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 0.16 (2101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.158 AC: 23948 AN: 151876 Hom.: 2090 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.158 AC: 23983 AN: 151994 Hom.: 2101 Cov.: 32 AF XY: 0.160 AC XY: 11857 AN XY: 74276

African (AFR) AF: 0.176 AC: 7283 AN: 41450

American (AMR) AF: 0.149 AC: 2280 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 343 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1672 AN: 5170

South Asian (SAS) AF: 0.165 AC: 798 AN: 4822

European-Finnish (FIN) AF: 0.151 AC: 1582 AN: 10500

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9570 AN: 67984

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.147 Hom.: 208

Bravo AF: 0.160

Asia WGS AF: 0.232 AC: 804 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.091
DANN	Benign	0.56
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10487799; hg19: chr7-15097731;