rs1329061

Variant names:

• chr9-117674839-G-A
• rs1329061

Your query was ambiguous. Multiple possible variants found:

• chr9-117674839-G-A
• chr9-117674839-G-C

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 0.528 in 151,794 control chromosomes in the GnomAD database, including 23,795 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 0.53 (23795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

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 (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.528 AC: 80090 AN: 151676 Hom.: 23802 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.528 AC: 80094 AN: 151794 Hom.: 23795 Cov.: 31 AF XY: 0.526 AC XY: 39048 AN XY: 74192

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.570

Alfa AF: 0.589 Hom.: 4755

Bravo AF: 0.520

Asia WGS AF: 0.590 AC: 2051 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1329061; hg19: chr9-120437117;