rs10157822

Variant names:

• chr1-161242119-T-C
• rs10157822

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 0.401 in 151,956 control chromosomes in the GnomAD database, including 12,663 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 0.40 (12663 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 9 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 = 0.599 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: 0.401 AC: 60828 AN: 151838 Hom.: 12642 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.401 AC: 60897 AN: 151956 Hom.: 12663 Cov.: 31 AF XY: 0.400 AC XY: 29719 AN XY: 74246

African (AFR) AF: 0.489 AC: 20274 AN: 41432

American (AMR) AF: 0.424 AC: 6468 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3182 AN: 5156

South Asian (SAS) AF: 0.390 AC: 1882 AN: 4822

European-Finnish (FIN) AF: 0.311 AC: 3286 AN: 10554

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23402 AN: 67946

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.375 Hom.: 15838

Bravo AF: 0.411

Asia WGS AF: 0.503 AC: 1748 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	3.0
DANN	Benign	0.63
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs10157822; hg19: chr1-161211909;