rs10512329

Variant names:

• chr9-104483819-T-C
• rs10512329

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 0.0542 in 152,270 control chromosomes in the GnomAD database, including 492 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 0.054 (492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 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: 0.0541 AC: 8226 AN: 152152 Hom.: 489 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0542 AC: 8251 AN: 152270 Hom.: 492 Cov.: 33 AF XY: 0.0564 AC XY: 4198 AN XY: 74456

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0224

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0351 Hom.: 33

Bravo AF: 0.0565

Asia WGS AF: 0.189 AC: 653 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512329; hg19: chr9-107246100;