2-226267064-C-A

Variant names:

• chr2-226267064-C-A
• rs964818

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 0.137 in 152,112 control chromosomes in the GnomAD database, including 1,718 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 (1718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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: 0.137 AC: 20882 AN: 151994 Hom.: 1711 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.137 AC: 20912 AN: 152112 Hom.: 1718 Cov.: 32 AF XY: 0.141 AC XY: 10507 AN XY: 74340

Gnomad4 AFR AF: 0.0799

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.134

Alfa AF: 0.146 Hom.: 816

Bravo AF: 0.136

Asia WGS AF: 0.379 AC: 1314 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.097
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964818; hg19: chr2-227131780;