rs4513299

Positions:

• chr2-114292241-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 0.401 in 151,896 control chromosomes in the GnomAD database, including 12,352 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 0.40 (12352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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: 0.401 AC: 60930 AN: 151778 Hom.: 12342 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.401 AC: 60974 AN: 151896 Hom.: 12352 Cov.: 31 AF XY: 0.399 AC XY: 29634 AN XY: 74246

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.388

Alfa AF: 0.408 Hom.: 7007

Bravo AF: 0.398

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4513299; hg19: chr2-115049818; COSMIC: COSV60094570;