rs1437432

Variant names:

• chr2-116994428-T-C
• rs1437432

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 0.306 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

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 (EAS) allele frequency at 95% confidence interval = 0.611 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: 0.306 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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.315

Alfa AF: 0.334 Hom.: 1892

Bravo AF: 0.300

Asia WGS AF: 0.404 AC: 1405 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	3.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437432; hg19: chr2-117752004;