2-117110281-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;