chr2-238205330-A-G

Variant names:

• chr2-238205330-A-G
• rs11694064

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 0.825 in 152,154 control chromosomes in the GnomAD database, including 51,977 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 0.83 (51977 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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: 0.825 AC: 125451 AN: 152036 Hom.: 51921 Cov.: 33

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.825 AC: 125569 AN: 152154 Hom.: 51977 Cov.: 33 AF XY: 0.828 AC XY: 61612 AN XY: 74400

African (AFR) AF: 0.839 AC: 34817 AN: 41502

American (AMR) AF: 0.858 AC: 13130 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5091 AN: 5186

South Asian (SAS) AF: 0.855 AC: 4127 AN: 4826

European-Finnish (FIN) AF: 0.795 AC: 8413 AN: 10582

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54213 AN: 67978

Other (OTH) AF: 0.836 AC: 1767 AN: 2114

Alfa AF: 0.816 Hom.: 6339

Bravo AF: 0.829

Asia WGS AF: 0.897 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.46
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11694064; hg19: chr2-239113971;