chr2-222080332-T-C

Variant names:

• chr2-222080332-T-C
• rs348987

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 0.436 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.417

Alfa AF: 0.488 Hom.: 5828

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348987; hg19: chr2-222945051;