rs1325127

Variant names:

• chr9-12668328-C-T
• rs1325127

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 0.572 in 152,042 control chromosomes in the GnomAD database, including 26,836 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 0.57 (26836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.572 AC: 86966 AN: 151924 Hom.: 26825 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.572 AC: 87007 AN: 152042 Hom.: 26836 Cov.: 33 AF XY: 0.573 AC XY: 42578 AN XY: 74308

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.581

Alfa AF: 0.643 Hom.: 41265

Bravo AF: 0.561

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325127; hg19: chr9-12668328;