7-44490467-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015332.4(NUDCD3):c.134G>A(p.Arg45His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,451,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015332.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUDCD3 | NM_015332.4 | c.134G>A | p.Arg45His | missense_variant | Exon 1 of 6 | ENST00000355451.8 | NP_056147.2 | |
NUDCD3 | XM_011515247.3 | c.134G>A | p.Arg45His | missense_variant | Exon 1 of 6 | XP_011513549.1 | ||
NUDCD3 | XM_017011908.2 | c.134G>A | p.Arg45His | missense_variant | Exon 1 of 4 | XP_016867397.1 | ||
NUDCD3 | XR_007059994.1 | n.192G>A | non_coding_transcript_exon_variant | Exon 1 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUDCD3 | ENST00000355451.8 | c.134G>A | p.Arg45His | missense_variant | Exon 1 of 6 | 1 | NM_015332.4 | ENSP00000347626.6 | ||
NUDCD3 | ENST00000464812.1 | n.140G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | |||||
NUDCD3 | ENST00000497978.1 | n.-202G>A | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000218 AC: 5AN: 229456Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125206
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1451518Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 721354
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.134G>A (p.R45H) alteration is located in exon 1 (coding exon 1) of the NUDCD3 gene. This alteration results from a G to A substitution at nucleotide position 134, causing the arginine (R) at amino acid position 45 to be replaced by a histidine (H). 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