rs41290104
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042724.2(NECTIN2):c.533C>A(p.Thr178Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001042724.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECTIN2 | NM_001042724.2 | c.533C>A | p.Thr178Lys | missense_variant | Exon 3 of 9 | ENST00000252483.10 | NP_001036189.1 | |
NECTIN2 | NM_002856.3 | c.533C>A | p.Thr178Lys | missense_variant | Exon 3 of 6 | NP_002847.1 | ||
NECTIN2 | XM_047439169.1 | c.533C>A | p.Thr178Lys | missense_variant | Exon 3 of 6 | XP_047295125.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECTIN2 | ENST00000252483.10 | c.533C>A | p.Thr178Lys | missense_variant | Exon 3 of 9 | 1 | NM_001042724.2 | ENSP00000252483.4 | ||
NECTIN2 | ENST00000252485.8 | c.533C>A | p.Thr178Lys | missense_variant | Exon 3 of 6 | 1 | ENSP00000252485.3 | |||
NECTIN2 | ENST00000591581.1 | c.53C>A | p.Thr18Lys | missense_variant | Exon 1 of 4 | 2 | ENSP00000465587.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250834Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135696
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at