rs10513332

Positions:

• chr3-148150339-A-C
• chr3-148150339-A-T

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 0.229 in 152,106 control chromosomes in the GnomAD database, including 4,497 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 0.23 (4497 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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: 0.229 AC: 34805 AN: 151988 Hom.: 4493 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.229 AC: 34829 AN: 152106 Hom.: 4497 Cov.: 33 AF XY: 0.227 AC XY: 16877 AN XY: 74354

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.217

Alfa AF: 0.132 Hom.: 301

Bravo AF: 0.234

Asia WGS AF: 0.138 AC: 479 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513332; hg19: chr3-147868126;