rs1329061

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;