chr1-222521094-A-T

Variant names:

• chr1-222521094-A-T
• rs10495191

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 0.273 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.238 AC: 9850 AN: 41458

American (AMR) AF: 0.243 AC: 3715 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3466

East Asian (EAS) AF: 0.337 AC: 1738 AN: 5162

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4820

European-Finnish (FIN) AF: 0.370 AC: 3921 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19653 AN: 68004

Other (OTH) AF: 0.258 AC: 544 AN: 2110

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

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