chr1-235979897-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002508.3(NID1):c.3434A>C(p.Lys1145Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002508.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NID1 | ENST00000264187.7 | c.3434A>C | p.Lys1145Thr | missense_variant | Exon 18 of 20 | 1 | NM_002508.3 | ENSP00000264187.6 | ||
NID1 | ENST00000366595.7 | c.3035A>C | p.Lys1012Thr | missense_variant | Exon 15 of 17 | 1 | ENSP00000355554.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461618Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727116
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3434A>C (p.K1145T) alteration is located in exon 18 (coding exon 18) of the NID1 gene. This alteration results from a A to C substitution at nucleotide position 3434, causing the lysine (K) at amino acid position 1145 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.