rs964818

Variant names:

• chr2-226267064-C-A
• rs964818

Your query was ambiguous. Multiple possible variants found:

• chr2-226267064-C-A
• chr2-226267064-C-G

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 0.137 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0799 AC: 3315 AN: 41510

American (AMR) AF: 0.174 AC: 2650 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1729 AN: 5152

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1460 AN: 10580

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

European-Non Finnish (NFE) AF: 0.141 AC: 9619 AN: 67996

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.145 Hom.: 887

Bravo AF: 0.136

Asia WGS AF: 0.379 AC: 1314 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.097
DANN	Benign	0.25
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs964818; hg19: chr2-227131780;