16-77741621-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001105663.3(NUDT7):c.388C>T(p.His130Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H130Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001105663.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT7 | NM_001105663.3 | c.388C>T | p.His130Tyr | missense_variant | 4/4 | ENST00000268533.9 | |
NUDT7 | NM_001243660.2 | c.343C>T | p.His115Tyr | missense_variant | 4/4 | ||
NUDT7 | NM_001243661.2 | c.229C>T | p.His77Tyr | missense_variant | 3/3 | ||
NUDT7 | NM_001243657.2 | c.482C>T | p.Pro161Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT7 | ENST00000268533.9 | c.388C>T | p.His130Tyr | missense_variant | 4/4 | 1 | NM_001105663.3 | P1 | |
ENST00000563690.1 | n.647G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152050Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248552Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134888
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460820Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726732
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.388C>T (p.H130Y) alteration is located in exon 4 (coding exon 4) of the NUDT7 gene. This alteration results from a C to T substitution at nucleotide position 388, causing the histidine (H) at amino acid position 130 to be replaced by a tyrosine (Y). 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