rs10499658

Variant names:

• chr7-47183968-G-A
• rs10499658

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 0.139 in 152,094 control chromosomes in the GnomAD database, including 1,473 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 0.14 (1473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 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: 0.140 AC: 21204 AN: 151978 Hom.: 1473 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.139 AC: 21207 AN: 152094 Hom.: 1473 Cov.: 32 AF XY: 0.141 AC XY: 10445 AN XY: 74338

African (AFR) AF: 0.144 AC: 5954 AN: 41460

American (AMR) AF: 0.107 AC: 1637 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.143 AC: 742 AN: 5174

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9380 AN: 68000

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.136 Hom.: 206

Bravo AF: 0.133

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.65
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10499658; hg19: chr7-47223566;