rs328862

Variant names:

• chr9-7725409-A-C
• rs328862

Your query was ambiguous. Multiple possible variants found:

• chr9-7725409-A-C
• chr9-7725409-A-G

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 0.939 in 152,052 control chromosomes in the GnomAD database, including 67,173 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 0.94 (67173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.940 AC: 142747 AN: 151934 Hom.: 67136 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.939 AC: 142840 AN: 152052 Hom.: 67173 Cov.: 32 AF XY: 0.940 AC XY: 69859 AN XY: 74320

African (AFR) AF: 0.893 AC: 37039 AN: 41490

American (AMR) AF: 0.924 AC: 14082 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3472

East Asian (EAS) AF: 0.949 AC: 4882 AN: 5146

South Asian (SAS) AF: 0.932 AC: 4484 AN: 4812

European-Finnish (FIN) AF: 0.982 AC: 10422 AN: 10610

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65515 AN: 67962

Other (OTH) AF: 0.935 AC: 1975 AN: 2112

Alfa AF: 0.952 Hom.: 88668

Bravo AF: 0.933

Asia WGS AF: 0.931 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs328862; hg19: chr9-7725409;