rs328862

chr9-7725409-A-Cchr9-7725409-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;