rs10948301

Variant names:

• chr6-46736730-C-T
• rs10948301

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 0.205 in 152,126 control chromosomes in the GnomAD database, including 3,533 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 0.20 (3533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.205 AC: 31144 AN: 152008 Hom.: 3524 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.205 AC: 31180 AN: 152126 Hom.: 3533 Cov.: 32 AF XY: 0.212 AC XY: 15772 AN XY: 74364

African (AFR) AF: 0.141 AC: 5852 AN: 41508

American (AMR) AF: 0.289 AC: 4420 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3466

East Asian (EAS) AF: 0.164 AC: 846 AN: 5172

South Asian (SAS) AF: 0.456 AC: 2193 AN: 4806

European-Finnish (FIN) AF: 0.228 AC: 2407 AN: 10580

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13765 AN: 67994

Other (OTH) AF: 0.221 AC: 467 AN: 2116

Alfa AF: 0.214 Hom.: 1601

Bravo AF: 0.197

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.62
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10948301; hg19: chr6-46704467;