rs2273431
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_007361.4(NID2):c.2259G>T(p.Glu753Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_007361.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NID2 | NM_007361.4 | c.2259G>T | p.Glu753Asp | missense_variant, splice_region_variant | 10/22 | ENST00000216286.10 | |
NID2 | XM_005267405.5 | c.2340G>T | p.Glu780Asp | missense_variant, splice_region_variant | 9/21 | ||
NID2 | XM_005267406.5 | c.2340G>T | p.Glu780Asp | missense_variant, splice_region_variant | 9/20 | ||
NID2 | XM_005267407.5 | c.2259G>T | p.Glu753Asp | missense_variant, splice_region_variant | 10/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NID2 | ENST00000216286.10 | c.2259G>T | p.Glu753Asp | missense_variant, splice_region_variant | 10/22 | 1 | NM_007361.4 | P1 | |
NID2 | ENST00000556572.1 | c.210G>T | p.Glu70Asp | missense_variant, splice_region_variant | 2/13 | 2 | |||
NID2 | ENST00000554284.1 | n.441G>T | splice_region_variant, non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461122Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0AN XY: 726844
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at