chr2-113141212-C-G

Position:

• chr2-113141212-C-G

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 0.352 in 148,950 control chromosomes in the GnomAD database, including 9,819 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 0.35 (9819 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.352 AC: 52459 AN: 148862 Hom.: 9806 Cov.: 28

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.352 AC: 52485 AN: 148950 Hom.: 9819 Cov.: 28 AF XY: 0.348 AC XY: 25190 AN XY: 72348

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.0911

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.382

Alfa AF: 0.163 Hom.: 261

Bravo AF: 0.344

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374281; hg19: chr2-113898789;