2-112798015-C-T

Variant names:

• chr2-112798015-C-T
• rs11687624

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 0.535 in 151,672 control chromosomes in the GnomAD database, including 22,082 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 0.54 (22082 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 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: 0.535 AC: 81138 AN: 151554 Hom.: 22067 Cov.: 30

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.535 AC: 81190 AN: 151672 Hom.: 22082 Cov.: 30 AF XY: 0.531 AC XY: 39353 AN XY: 74090

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.536

Alfa AF: 0.563 Hom.: 32445

Bravo AF: 0.527

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11687624; hg19: chr2-113555592;