rs10513336

Variant names:

• chr3-148650600-A-C
• rs10513336

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 0.073 in 152,160 control chromosomes in the GnomAD database, including 549 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 0.073 (549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0729 AC: 11085 AN: 152042 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0783

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

GnomAD4 genome AF: 0.0730 AC: 11113 AN: 152160 Hom.: 549 Cov.: 32 AF XY: 0.0734 AC XY: 5459 AN XY: 74420

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0401

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.0414

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0392

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0780

Alfa AF: 0.0626 Hom.: 113

Bravo AF: 0.0731

Asia WGS AF: 0.0840 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513336; hg19: chr3-148368387;