chr2-114974-C-T

Variant names:

• chr2-114974-C-T
• rs876724

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.163 AC: 6749 AN: 41464

American (AMR) AF: 0.273 AC: 4174 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3462

East Asian (EAS) AF: 0.425 AC: 2194 AN: 5168

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3797 AN: 10538

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20908 AN: 67966

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.293 Hom.: 12237

Bravo AF: 0.258

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs876724; hg19: chr2-114974;