rs10507713

Variant names:

• chr13-64539514-A-G
• rs10507713

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 0.0416 in 151,852 control chromosomes in the GnomAD database, including 324 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 0.042 (324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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: 0.0415 AC: 6300 AN: 151734 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.00665

Gnomad EAS AF: 0.00214

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00727

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0416 AC: 6318 AN: 151852 Hom.: 324 Cov.: 32 AF XY: 0.0409 AC XY: 3040 AN XY: 74238

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.00665

Gnomad4 EAS AF: 0.00214

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00725

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0307 Hom.: 32

Bravo AF: 0.0455

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.052
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507713; hg19: chr13-65113646;