13-42660678-A-G

Variant names:

• chr13-42660678-A-G
• rs10507514

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 0.3 in 152,136 control chromosomes in the GnomAD database, including 7,080 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 0.30 (7080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.300 AC: 45612 AN: 152018 Hom.: 7065 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.300 AC: 45663 AN: 152136 Hom.: 7080 Cov.: 33 AF XY: 0.297 AC XY: 22090 AN XY: 74364

African (AFR) AF: 0.275 AC: 11421 AN: 41496

American (AMR) AF: 0.223 AC: 3418 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2390 AN: 5182

South Asian (SAS) AF: 0.229 AC: 1101 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3211 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22149 AN: 67982

Other (OTH) AF: 0.269 AC: 569 AN: 2112

Alfa AF: 0.313 Hom.: 3211

Bravo AF: 0.295

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10507514; hg19: chr13-43234814;