rs10493476

Positions:

• chr1-70632831-G-A

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 0.0394 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.0410

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0316

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.0407

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493476; hg19: chr1-71098514;