2-218161368-G-A

Variant names:

• chr2-218161368-G-A
• rs1467142

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 0.913 in 151,046 control chromosomes in the GnomAD database, including 63,354 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 0.91 (63354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 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: 0.913 AC: 137791 AN: 150930 Hom.: 63322 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.913 AC: 137877 AN: 151046 Hom.: 63354 Cov.: 31 AF XY: 0.911 AC XY: 67269 AN XY: 73806

African (AFR) AF: 0.857 AC: 34640 AN: 40426

American (AMR) AF: 0.885 AC: 13476 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3365 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4782 AN: 5182

South Asian (SAS) AF: 0.891 AC: 4292 AN: 4818

European-Finnish (FIN) AF: 0.943 AC: 9983 AN: 10592

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64209 AN: 68026

Other (OTH) AF: 0.929 AC: 1949 AN: 2098

Alfa AF: 0.908 Hom.: 3922

Bravo AF: 0.907

Asia WGS AF: 0.909 AC: 3163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.54
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1467142; hg19: chr2-219026091;