rs10513336

Positions:

• chr3-148650600-A-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 0.073 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;