rs1478129

Variant names:

• chr2-193692341-C-T
• rs1478129

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 0.159 in 151,354 control chromosomes in the GnomAD database, including 2,424 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 0.16 (2424 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.159 AC: 24057 AN: 151238 Hom.: 2427 Cov.: 30

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.159 AC: 24048 AN: 151354 Hom.: 2424 Cov.: 30 AF XY: 0.156 AC XY: 11527 AN XY: 73928

Gnomad4 AFR AF: 0.0497

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.206

Alfa AF: 0.214 Hom.: 4822

Bravo AF: 0.155

Asia WGS AF: 0.104 AC: 362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.8
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478129; hg19: chr2-194557065;