rs9328554

Variant names:

• chr10-125448240-C-T
• rs9328554

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 0.737 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.755

Alfa AF: 0.781 Hom.: 21236

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9328554; hg19: chr10-127136809;