rs1325127

chr9-12668328-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 0.572 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;