rs11879589

Positions:

• chr19-44870019-G-A
• chr19-44870019-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042724.2(NECTIN2):​c.479-1834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,130 control chromosomes in the GnomAD database, including 1,901 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 (1901 hom., cov: 31)
• Consequence: NECTIN2 NM_001042724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

NECTIN2 (HGNC:9707): (nectin cell adhesion molecule 2) This gene encodes a single-pass type I membrane glycoprotein with two Ig-like C2-type domains and an Ig-like V-type domain. This protein is one of the plasma membrane components of adherens junctions. It also serves as an entry for certain mutant strains of herpes simplex virus and pseudorabies virus, and it is involved in cell to cell spreading of these viruses. Variations in this gene have been associated with differences in the severity of multiple sclerosis. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NECTIN2	NM_001042724.2	c.479-1834G>A		intron_variant		ENST00000252483.10	NP_001036189.1
NECTIN2	NM_002856.3	c.479-1834G>A		intron_variant			NP_002847.1
NECTIN2	XM_047439169.1	c.479-1834G>A		intron_variant			XP_047295125.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECTIN2	ENST00000252483.10	c.479-1834G>A		intron_variant		1	NM_001042724.2	ENSP00000252483	P3
NECTIN2	ENST00000252485.8	c.479-1834G>A		intron_variant		1		ENSP00000252485	A2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21709 AN: 152012 Hom.: 1893 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.143 AC: 21749 AN: 152130 Hom.: 1901 Cov.: 31 AF XY: 0.143 AC XY: 10664 AN XY: 74370

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.149

Alfa AF: 0.102 Hom.: 1369

Bravo AF: 0.154

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11879589; hg19: chr19-45373276;