rs10507713

Positions:

• chr13-64539514-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;