NM_002855.5:c.1328_1333dupAGGAGG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002855.5(NECTIN1):c.1328_1333dupAGGAGG(p.Glu443_Glu444dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00404 in 1,610,616 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002855.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECTIN1 | NM_002855.5 | c.1328_1333dupAGGAGG | p.Glu443_Glu444dup | conservative_inframe_insertion | Exon 6 of 6 | ENST00000264025.8 | NP_002846.3 | |
NECTIN1 | NM_203285.2 | c.1003+10186_1003+10191dupAGGAGG | intron_variant | Intron 5 of 7 | NP_976030.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECTIN1 | ENST00000264025.8 | c.1328_1333dupAGGAGG | p.Glu443_Glu444dup | conservative_inframe_insertion | Exon 6 of 6 | 1 | NM_002855.5 | ENSP00000264025.3 | ||
NECTIN1 | ENST00000341398.6 | n.1003+10186_1003+10191dupAGGAGG | intron_variant | Intron 5 of 7 | 1 | |||||
NECTIN1 | ENST00000531468.2 | c.1003+10186_1003+10191dupAGGAGG | intron_variant | Intron 5 of 9 | 3 | ENSP00000513010.1 |
Frequencies
GnomAD3 genomes AF: 0.00300 AC: 454AN: 151558Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00299 AC: 689AN: 230564Hom.: 0 AF XY: 0.00278 AC XY: 347AN XY: 124844
GnomAD4 exome AF: 0.00414 AC: 6047AN: 1458942Hom.: 11 Cov.: 39 AF XY: 0.00402 AC XY: 2919AN XY: 725782
GnomAD4 genome AF: 0.00298 AC: 452AN: 151674Hom.: 0 Cov.: 31 AF XY: 0.00305 AC XY: 226AN XY: 74102
ClinVar
Submissions by phenotype
NECTIN1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at