rs9328554

Variant names:

• chr10-125448240-C-T
• rs9328554

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 0.737 in 152,116 control chromosomes in the GnomAD database, including 41,993 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 0.74 (41993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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: 0.737 AC: 111996 AN: 151998 Hom.: 41959 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.737 AC: 112084 AN: 152116 Hom.: 41993 Cov.: 33 AF XY: 0.737 AC XY: 54819 AN XY: 74354

African (AFR) AF: 0.593 AC: 24583 AN: 41450

American (AMR) AF: 0.805 AC: 12321 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4683 AN: 5180

South Asian (SAS) AF: 0.776 AC: 3745 AN: 4828

European-Finnish (FIN) AF: 0.723 AC: 7643 AN: 10564

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53713 AN: 68002

Other (OTH) AF: 0.755 AC: 1597 AN: 2114

Alfa AF: 0.781 Hom.: 23830

Bravo AF: 0.737

Asia WGS AF: 0.822 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9328554; hg19: chr10-127136809;