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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531468.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN1	ENST00000531468.2	TSL:3	c.1342-2490T>G		intron	N/A	ENSP00000513010.1	A0A8V8TKI1
	USP2-AS1	ENST00000706362.2		n.581-5159A>C		intron	N/A
	USP2-AS1	ENST00000706364.1		n.306+330A>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1567375;

hg19: chr11-119502477;