chr2-226269179-G-A

Variant names:

• chr2-226269179-G-A
• rs10498199

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 0.138 in 152,012 control chromosomes in the GnomAD database, including 1,728 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 0.14 (1728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.138 AC: 20957 AN: 151894 Hom.: 1721 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.138 AC: 20987 AN: 152012 Hom.: 1728 Cov.: 32 AF XY: 0.142 AC XY: 10563 AN XY: 74304

African (AFR) AF: 0.0803 AC: 3329 AN: 41478

American (AMR) AF: 0.174 AC: 2657 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1729 AN: 5142

South Asian (SAS) AF: 0.245 AC: 1183 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10556

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9648 AN: 67976

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.0677 Hom.: 91

Bravo AF: 0.136

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.53
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs10498199; hg19: chr2-227133895;