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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.940 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

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.935

Alfa AF: 0.955 Hom.: 68406

Bravo AF: 0.933

Asia WGS AF: 0.931 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs328862; hg19: chr9-7725409;