2-226495730-T-C

Variant names:

• chr2-226495730-T-C
• rs11903929

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 0.183 in 152,148 control chromosomes in the GnomAD database, including 3,753 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 0.18 (3753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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: 0.182 AC: 27734 AN: 152030 Hom.: 3741 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.183 AC: 27805 AN: 152148 Hom.: 3753 Cov.: 32 AF XY: 0.188 AC XY: 14006 AN XY: 74382

African (AFR) AF: 0.287 AC: 11906 AN: 41498

American (AMR) AF: 0.212 AC: 3247 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3472

East Asian (EAS) AF: 0.667 AC: 3441 AN: 5156

South Asian (SAS) AF: 0.205 AC: 987 AN: 4816

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10608

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6099 AN: 67988

Other (OTH) AF: 0.174 AC: 368 AN: 2116

Alfa AF: 0.124 Hom.: 4876

Bravo AF: 0.199

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.35
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11903929; hg19: chr2-227360446;