chr2-114974-C-T

Variant names:

• chr2-114974-C-T
• rs876724

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 0.269 in 152,012 control chromosomes in the GnomAD database, including 5,832 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 0.27 (5832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.270 AC: 40969 AN: 151894 Hom.: 5838 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.269 AC: 40953 AN: 152012 Hom.: 5832 Cov.: 32 AF XY: 0.272 AC XY: 20233 AN XY: 74270

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.265

Alfa AF: 0.290 Hom.: 1855

Bravo AF: 0.258

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs876724; hg19: chr2-114974;