2-222079226-C-T

Variant names:

• chr2-222079226-C-T
• rs348970

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 0.448 in 152,002 control chromosomes in the GnomAD database, including 16,016 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 0.45 (16016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.448 AC: 68015 AN: 151884 Hom.: 16011 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.448 AC: 68062 AN: 152002 Hom.: 16016 Cov.: 32 AF XY: 0.444 AC XY: 32950 AN XY: 74264

African (AFR) AF: 0.318 AC: 13182 AN: 41452

American (AMR) AF: 0.376 AC: 5743 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1646 AN: 5172

South Asian (SAS) AF: 0.396 AC: 1908 AN: 4814

European-Finnish (FIN) AF: 0.559 AC: 5901 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.537 AC: 36494 AN: 67958

Other (OTH) AF: 0.429 AC: 906 AN: 2114

Alfa AF: 0.497 Hom.: 36769

Bravo AF: 0.431

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.8
DANN	Benign	0.79
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs348970; hg19: chr2-222943945;