rs10933144

chr2-226398692-A-G

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 0.272 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

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 = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.295

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10933144; hg19: chr2-227263408;