rs6480947

Variant names:

• chr10-79476454-A-G
• rs6480947

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 0.179 in 152,210 control chromosomes in the GnomAD database, including 2,596 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 0.18 (2596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 2 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 = 0.205 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: 0.179 AC: 27232 AN: 152092 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.179 AC: 27268 AN: 152210 Hom.: 2596 Cov.: 32 AF XY: 0.182 AC XY: 13535 AN XY: 74426

African (AFR) AF: 0.188 AC: 7800 AN: 41528

American (AMR) AF: 0.117 AC: 1792 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3470

East Asian (EAS) AF: 0.178 AC: 922 AN: 5188

South Asian (SAS) AF: 0.216 AC: 1044 AN: 4830

European-Finnish (FIN) AF: 0.210 AC: 2220 AN: 10582

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 12038 AN: 67998

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.147 Hom.: 2330

Bravo AF: 0.167

Asia WGS AF: 0.184 AC: 645 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	0.12
DANN	Benign	0.54
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6480947; hg19: chr10-81236210;