2-222079226-C-T

Variant names:

• chr2-222079226-C-T
• rs348970

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 0.448 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.448 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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.429

Alfa AF: 0.506 Hom.: 27812

Bravo AF: 0.431

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348970; hg19: chr2-222943945;