rs13355929

Variant names:

• chr5-141879468-C-T
• rs13355929
• ENST00000760571.1:n.56+1780C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000760571.1(ENSG00000287726):​n.56+1780C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,172 control chromosomes in the GnomAD database, including 2,423 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 0.11 (2423 hom., cov: 32)
• Consequence: ENSG00000287726 ENST00000760571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 0 publications found

Genes affected

ENSG00000287726 (HGNC:):

PCDH1 (HGNC:8655): (protocadherin 1) This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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
ENSG00000287726	ENST00000760571.1	n.56+1780C>T		intron_variant	Intron 1 of 3
PCDH1	ENST00000514773.1	c.-323G>A		upstream_gene_variant		4		ENSP00000424163.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16682 AN: 152054 Hom.: 2421 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0223

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.110 AC: 16710 AN: 152172 Hom.: 2423 Cov.: 32 AF XY: 0.106 AC XY: 7868 AN XY: 74404

African (AFR) AF: 0.332 AC: 13780 AN: 41478

American (AMR) AF: 0.0535 AC: 819 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4824

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0223 AC: 1518 AN: 68008

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0456 Hom.: 1014

Bravo AF: 0.123

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		-0.36
PromoterAI		0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13355929; hg19: chr5-141259033;