13-64539514-A-G

Variant names:

• chr13-64539514-A-G
• rs10507713

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.122 AC: 5068 AN: 41466

American (AMR) AF: 0.0199 AC: 302 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.00665 AC: 23 AN: 3458

East Asian (EAS) AF: 0.00214 AC: 11 AN: 5132

South Asian (SAS) AF: 0.0729 AC: 352 AN: 4830

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10622

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00725 AC: 492 AN: 67816

Other (OTH) AF: 0.0265 AC: 56 AN: 2110

Alfa AF: 0.0543 Hom.: 172

Bravo AF: 0.0455

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.052
DANN	Benign	0.53
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10507713; hg19: chr13-65113646;