2-116994428-T-C

Variant names:

• chr2-116994428-T-C
• rs1437432

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 0.306 in 152,016 control chromosomes in the GnomAD database, including 8,014 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 0.31 (8014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46551 AN: 151896 Hom.: 8018 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.306 AC: 46549 AN: 152016 Hom.: 8014 Cov.: 32 AF XY: 0.308 AC XY: 22903 AN XY: 74272

African (AFR) AF: 0.162 AC: 6708 AN: 41486

American (AMR) AF: 0.325 AC: 4955 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3233 AN: 5136

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4826

European-Finnish (FIN) AF: 0.360 AC: 3798 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24230 AN: 67970

Other (OTH) AF: 0.315 AC: 665 AN: 2108

Alfa AF: 0.340 Hom.: 3607

Bravo AF: 0.300

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.38
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs1437432; hg19: chr2-117752004;