chr13-113102878-C-A

Variant names:

• chr13-113102878-C-A
• rs1755685

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 0.139 in 152,168 control chromosomes in the GnomAD database, including 1,627 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 0.14 (1627 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 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: 0.139 AC: 21113 AN: 152050 Hom.: 1627 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.139 AC: 21127 AN: 152168 Hom.: 1627 Cov.: 33 AF XY: 0.138 AC XY: 10295 AN XY: 74386

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0392

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.155

Alfa AF: 0.131 Hom.: 1345

Bravo AF: 0.142

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1755685; hg19: chr13-113757192;