13-113105172-A-C

Variant names:

• chr13-113105172-A-C
• rs762635

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 0.207 in 151,894 control chromosomes in the GnomAD database, including 3,819 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 0.21 (3819 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.207 AC: 31406 AN: 151776 Hom.: 3809 Cov.: 30

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.207 AC: 31436 AN: 151894 Hom.: 3819 Cov.: 30 AF XY: 0.211 AC XY: 15688 AN XY: 74246

African (AFR) AF: 0.105 AC: 4332 AN: 41388

American (AMR) AF: 0.257 AC: 3921 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2320 AN: 5168

South Asian (SAS) AF: 0.156 AC: 750 AN: 4804

European-Finnish (FIN) AF: 0.323 AC: 3410 AN: 10546

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15771 AN: 67932

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.209 Hom.: 426

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.93
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs762635; hg19: chr13-113759486;