14-52011568-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007361.4(NID2):c.3536C>T(p.Thr1179Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000985 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007361.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NID2 | NM_007361.4 | c.3536C>T | p.Thr1179Met | missense_variant | 17/22 | ENST00000216286.10 | NP_031387.3 | |
NID2 | XM_005267405.5 | c.3617C>T | p.Thr1206Met | missense_variant | 16/21 | XP_005267462.1 | ||
NID2 | XM_005267406.5 | c.3473C>T | p.Thr1158Met | missense_variant | 15/20 | XP_005267463.1 | ||
NID2 | XM_005267407.5 | c.3392C>T | p.Thr1131Met | missense_variant | 16/21 | XP_005267464.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NID2 | ENST00000216286.10 | c.3536C>T | p.Thr1179Met | missense_variant | 17/22 | 1 | NM_007361.4 | ENSP00000216286.4 | ||
NID2 | ENST00000556572.1 | c.1340C>T | p.Thr447Met | missense_variant | 8/13 | 2 | ENSP00000452190.1 | |||
NID2 | ENST00000553297.1 | n.454C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251406Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135886
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.0000935 AC XY: 68AN XY: 727234
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.3536C>T (p.T1179M) alteration is located in exon 17 (coding exon 17) of the NID2 gene. This alteration results from a C to T substitution at nucleotide position 3536, causing the threonine (T) at amino acid position 1179 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at