19-44885967-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001042724.2(NECTIN2):c.1227G>C(p.Pro409=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000374 in 1,602,548 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
Consequence
NM_001042724.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECTIN2 | NM_001042724.2 | c.1227G>C | p.Pro409= | synonymous_variant | 7/9 | ENST00000252483.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECTIN2 | ENST00000252483.10 | c.1227G>C | p.Pro409= | synonymous_variant | 7/9 | 1 | NM_001042724.2 | P3 | |
ENST00000585408.1 | n.115-3629C>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
NECTIN2 | ENST00000592018.1 | c.28-2143G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1450434Hom.: 0 Cov.: 32 AF XY: 0.00000415 AC XY: 3AN XY: 722248
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at