rs10484761

Variant names:

• chr6-40834522-T-C
• rs10484761

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 0.304 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.304 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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.307

Alfa AF: 0.225 Hom.: 2311

Bravo AF: 0.310

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484761; hg19: chr6-40802261;