2-117110281-C-T

Variant names:

• chr2-117110281-C-T
• rs332880

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 0.798 in 151,840 control chromosomes in the GnomAD database, including 48,592 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 0.80 (48592 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.892 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: 0.798 AC: 121097 AN: 151722 Hom.: 48544 Cov.: 29

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.798 AC: 121202 AN: 151840 Hom.: 48592 Cov.: 29 AF XY: 0.803 AC XY: 59557 AN XY: 74188

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.785

Alfa AF: 0.795 Hom.: 22822

Bravo AF: 0.803

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs332880; hg19: chr2-117867857; COSMIC: COSV60099648;