rs10493476

Variant names:

• chr1-70632831-G-A
• rs10493476

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 0.0394 in 151,428 control chromosomes in the GnomAD database, including 284 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 0.039 (284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.0393 AC: 5952 AN: 151316 Hom.: 277 Cov.: 31

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0394 AC: 5972 AN: 151428 Hom.: 284 Cov.: 31 AF XY: 0.0428 AC XY: 3164 AN XY: 73902

African (AFR) AF: 0.0119 AC: 490 AN: 41310

American (AMR) AF: 0.0737 AC: 1120 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0410 AC: 142 AN: 3462

East Asian (EAS) AF: 0.252 AC: 1298 AN: 5142

South Asian (SAS) AF: 0.117 AC: 561 AN: 4784

European-Finnish (FIN) AF: 0.0316 AC: 328 AN: 10376

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0285 AC: 1937 AN: 67862

Other (OTH) AF: 0.0407 AC: 85 AN: 2088

Alfa AF: 0.0292 Hom.: 11

Bravo AF: 0.0422

Asia WGS AF: 0.157 AC: 543 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.65
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10493476; hg19: chr1-71098514;