2-218161368-G-A

Position:

• chr2-218161368-G-A

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 0.913 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.929

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1467142; hg19: chr2-219026091;