rs10513432

Positions:

• chr3-152817576-T-C

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 0.115 in 152,184 control chromosomes in the GnomAD database, including 1,909 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 0.11 (1909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17451 AN: 152066 Hom.: 1901 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.115 AC: 17500 AN: 152184 Hom.: 1909 Cov.: 32 AF XY: 0.114 AC XY: 8472 AN XY: 74426

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0676

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0915

Alfa AF: 0.0484 Hom.: 669

Bravo AF: 0.122

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
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: rs10513432; hg19: chr3-152535365;