rs1329387

Variant names:

• chr9-81383132-C-T
• rs1329387

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.708 in 152,074 control chromosomes in the GnomAD database, including 38,961 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 0.71 (38961 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.708 AC: 107650 AN: 151956 Hom.: 38937 Cov.: 33

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.708 AC: 107704 AN: 152074 Hom.: 38961 Cov.: 33 AF XY: 0.705 AC XY: 52435 AN XY: 74348

African (AFR) AF: 0.811 AC: 33637 AN: 41484

American (AMR) AF: 0.581 AC: 8874 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2662 AN: 3464

East Asian (EAS) AF: 0.360 AC: 1857 AN: 5162

South Asian (SAS) AF: 0.684 AC: 3296 AN: 4822

European-Finnish (FIN) AF: 0.682 AC: 7219 AN: 10582

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47872 AN: 67976

Other (OTH) AF: 0.677 AC: 1431 AN: 2114

Alfa AF: 0.698 Hom.: 61483

Bravo AF: 0.701

Asia WGS AF: 0.553 AC: 1926 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	2.1
DANN	Benign	0.44
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1329387; hg19: chr9-83998047; COSMIC: COSV60368057;