rs1478129

Positions:

• chr2-193692341-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;