19-44878777-A-T

Variant names:

• chr19-44878777-A-T
• rs6859
• ENST00000252485.8:c.*157A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000252485.8(NECTIN2):​c.*157A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000785 in 1,273,202 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 7.9e-7 (0 hom.)
• Consequence: NECTIN2 ENST00000252485.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 168 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000252485.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN2	NM_001042724.2	MANE Select	c.1043-3434A>T		intron	N/A	NP_001036189.1
	NECTIN2	NM_002856.3		c.*157A>T		3_prime_UTR	Exon 6 of 6	NP_002847.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN2	ENST00000252485.8	TSL:1	c.*157A>T		3_prime_UTR	Exon 6 of 6	ENSP00000252485.3
	NECTIN2	ENST00000252483.10	TSL:1 MANE Select	c.1043-3434A>T		intron	N/A	ENSP00000252483.4
	NECTIN2	ENST00000591581.1	TSL:2	c.*157A>T		3_prime_UTR	Exon 4 of 4	ENSP00000465587.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 7.85e-7 AC: 1 AN: 1273202 Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0 AN XY: 615992

African (AFR) AF: 0.00 AC: 0 AN: 28080

American (AMR) AF: 0.00 AC: 0 AN: 19134

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18604

East Asian (EAS) AF: 0.00 AC: 0 AN: 34276

South Asian (SAS) AF: 0.00 AC: 0 AN: 59954

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29910

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3952

European-Non Finnish (NFE) AF: 9.74e-7 AC: 1 AN: 1026362

Other (OTH) AF: 0.00 AC: 0 AN: 52930

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs6859; hg19: chr19-45382034;