rs1567375

Variant names:

• chr11-119631766-A-C
• rs1567375
• ENST00000531468.2:c.1342-2490T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-119631766-A-C
• chr11-119631766-A-G

Variant summary

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

The ENST00000531468.2(NECTIN1):​c.1342-2490T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,026 control chromosomes in the GnomAD database, including 25,977 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 0.58 (25977 hom., cov: 32)
• Consequence: NECTIN1 ENST00000531468.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 6 publications found

Genes affected

NECTIN1 (HGNC:9706): (nectin cell adhesion molecule 1) This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]

USP2-AS1 (HGNC:48673): (USP2 antisense RNA 1)

LOC105369520 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369520	XR_001748413.1	n.60+330A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN1	ENST00000531468.2	c.1342-2490T>G		intron_variant	Intron 8 of 9	3		ENSP00000513010.1
USP2-AS1	ENST00000706362.2	n.581-5159A>C		intron_variant	Intron 4 of 4
USP2-AS1	ENST00000706364.1	n.306+330A>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88595 AN: 151908 Hom.: 25939 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.583 AC: 88685 AN: 152026 Hom.: 25977 Cov.: 32 AF XY: 0.580 AC XY: 43089 AN XY: 74310

African (AFR) AF: 0.605 AC: 25075 AN: 41470

American (AMR) AF: 0.623 AC: 9507 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1684 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2939 AN: 5140

South Asian (SAS) AF: 0.420 AC: 2024 AN: 4814

European-Finnish (FIN) AF: 0.601 AC: 6362 AN: 10588

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39250 AN: 67966

Other (OTH) AF: 0.568 AC: 1196 AN: 2104

Alfa AF: 0.551 Hom.: 10688

Bravo AF: 0.588

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1567375; hg19: chr11-119502477;