rs2671222

Variant names:

• chr2-218167879-T-C
• rs2671222

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 0.897 in 152,216 control chromosomes in the GnomAD database, including 61,481 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 0.90 (61481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136417 AN: 152098 Hom.: 61454 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.897 AC: 136499 AN: 152216 Hom.: 61481 Cov.: 32 AF XY: 0.896 AC XY: 66654 AN XY: 74422

African (AFR) AF: 0.802 AC: 33306 AN: 41512

American (AMR) AF: 0.878 AC: 13423 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3371 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4754 AN: 5152

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4828

European-Finnish (FIN) AF: 0.943 AC: 10003 AN: 10610

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

European-Non Finnish (NFE) AF: 0.944 AC: 64222 AN: 68030

Other (OTH) AF: 0.915 AC: 1934 AN: 2114

Alfa AF: 0.907 Hom.: 23413

Bravo AF: 0.888

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.021
DANN	Benign	0.36
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2671222; hg19: chr2-219032602;