rs878129

Variant names:

• chr1-113916573-C-T
• rs878129

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 0.195 in 152,128 control chromosomes in the GnomAD database, including 3,677 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 0.19 (3677 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 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: 0.195 AC: 29588 AN: 152010 Hom.: 3676 Cov.: 31

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.195 AC: 29589 AN: 152128 Hom.: 3677 Cov.: 31 AF XY: 0.199 AC XY: 14774 AN XY: 74358

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.186

Alfa AF: 0.230 Hom.: 2309

Bravo AF: 0.178

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878129; hg19: chr1-114459195;