rs10487799

Positions:

• chr7-15058106-G-A

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 0.158 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.144

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487799; hg19: chr7-15097731;