rs10513332

Variant names:

• chr3-148150339-A-C
• rs10513332

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;