rs10484761

Variant names:

• chr6-40834522-T-C
• rs10484761

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 0.304 in 151,896 control chromosomes in the GnomAD database, including 7,849 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 0.30 (7849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46092 AN: 151778 Hom.: 7836 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.304 AC: 46132 AN: 151896 Hom.: 7849 Cov.: 31 AF XY: 0.303 AC XY: 22520 AN XY: 74264

African (AFR) AF: 0.462 AC: 19103 AN: 41368

American (AMR) AF: 0.276 AC: 4219 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3466

East Asian (EAS) AF: 0.123 AC: 636 AN: 5164

South Asian (SAS) AF: 0.155 AC: 746 AN: 4812

European-Finnish (FIN) AF: 0.308 AC: 3243 AN: 10546

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15925 AN: 67954

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.252 Hom.: 5892

Bravo AF: 0.310

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.059
DANN	Benign	0.36
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10484761; hg19: chr6-40802261;