chr2-112766390-C-T

Variant names:

• chr2-112766390-C-T
• rs2048874

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 0.101 in 152,184 control chromosomes in the GnomAD database, including 866 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 0.10 (866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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: 0.101 AC: 15383 AN: 152066 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.101 AC: 15396 AN: 152184 Hom.: 866 Cov.: 32 AF XY: 0.100 AC XY: 7440 AN XY: 74400

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.116

Alfa AF: 0.119 Hom.: 1614

Bravo AF: 0.0991

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048874; hg19: chr2-113523967;