rs2494752

Variant names:

• chr14-104797271-A-G
• rs2494752

Your query was ambiguous. Multiple possible variants found:

• chr14-104797271-A-G
• chr14-104797271-A-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 0.843 in 152,246 control chromosomes in the GnomAD database, including 55,305 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 0.84 (55305 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92

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 (NFE) allele frequency at 95% confidence interval = 0.917 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: 0.843 AC: 128227 AN: 152128 Hom.: 55262 Cov.: 34

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.843 AC: 128334 AN: 152246 Hom.: 55305 Cov.: 34 AF XY: 0.836 AC XY: 62239 AN XY: 74458

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.844

Alfa AF: 0.901 Hom.: 73287

Bravo AF: 0.831

Asia WGS AF: 0.495 AC: 1727 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	0.43
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494752; hg19: chr14-105263608;