rs4325129

Variant names:

• chr1-159492591-A-G
• rs4325129

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 152,218 control chromosomes in the GnomAD database, including 2,469 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 (2469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 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: 24241 AN: 152100 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.159 AC: 24249 AN: 152218 Hom.: 2469 Cov.: 32 AF XY: 0.162 AC XY: 12059 AN XY: 74406

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0779

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.145

Alfa AF: 0.195 Hom.: 4962

Bravo AF: 0.146

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4325129; hg19: chr1-159462381;