rs10495191

Positions:

• chr1-222521094-A-T

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 0.273 in 152,084 control chromosomes in the GnomAD database, including 5,828 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 0.27 (5828 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.222521094A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41467 AN: 151966 Hom.: 5825 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.273 AC: 41497 AN: 152084 Hom.: 5828 Cov.: 32 AF XY: 0.274 AC XY: 20379 AN XY: 74344

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.258

Alfa AF: 0.282 Hom.: 744

Bravo AF: 0.264

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495191; hg19: chr1-222694436; COSMIC: COSV58563887;