rs10933144

Variant names:

• chr2-226398692-A-G
• rs10933144

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 0.272 in 152,004 control chromosomes in the GnomAD database, including 6,470 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 (6470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 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 = 0.726 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: 0.272 AC: 41261 AN: 151886 Hom.: 6458 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.272 AC: 41295 AN: 152004 Hom.: 6470 Cov.: 32 AF XY: 0.275 AC XY: 20402 AN XY: 74316

African (AFR) AF: 0.314 AC: 13032 AN: 41448

American (AMR) AF: 0.301 AC: 4601 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3468

East Asian (EAS) AF: 0.746 AC: 3843 AN: 5152

South Asian (SAS) AF: 0.254 AC: 1228 AN: 4830

European-Finnish (FIN) AF: 0.221 AC: 2331 AN: 10552

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14390 AN: 67970

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.253 Hom.: 986

Bravo AF: 0.283

Asia WGS AF: 0.453 AC: 1572 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	0.042
DANN	Benign	0.89
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10933144; hg19: chr2-227263408;