2-222080332-T-C

Variant names:

• chr2-222080332-T-C
• rs348987

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 0.436 in 152,168 control chromosomes in the GnomAD database, including 15,511 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 0.44 (15511 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• 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: 0.436 AC: 66246 AN: 152050 Hom.: 15507 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.436 AC: 66290 AN: 152168 Hom.: 15511 Cov.: 33 AF XY: 0.432 AC XY: 32125 AN XY: 74394

African (AFR) AF: 0.276 AC: 11479 AN: 41520

American (AMR) AF: 0.371 AC: 5664 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1654 AN: 5184

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4820

European-Finnish (FIN) AF: 0.557 AC: 5894 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36484 AN: 67990

Other (OTH) AF: 0.417 AC: 882 AN: 2116

Alfa AF: 0.486 Hom.: 7194

Bravo AF: 0.416

Asia WGS AF: 0.384 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.9
DANN	Benign	0.70
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs348987; hg19: chr2-222945051;