rs1755685

Variant names:

• chr13-113102878-C-A
• rs1755685

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 0.139 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.179 AC: 7416 AN: 41490

American (AMR) AF: 0.126 AC: 1925 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3470

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5182

South Asian (SAS) AF: 0.269 AC: 1298 AN: 4824

European-Finnish (FIN) AF: 0.0758 AC: 803 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8260 AN: 67998

Other (OTH) AF: 0.155 AC: 328 AN: 2116

Alfa AF: 0.136 Hom.: 2028

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1755685; hg19: chr13-113757192;