chr16-77741623-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001105663.3(NUDT7):c.390C>G(p.His130Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,172 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. H130Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001105663.3 missense
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 |
---|---|---|---|---|---|---|---|
NUDT7 | NM_001105663.3 | c.390C>G | p.His130Gln | missense_variant | 4/4 | ENST00000268533.9 | |
NUDT7 | NM_001243660.2 | c.345C>G | p.His115Gln | missense_variant | 4/4 | ||
NUDT7 | NM_001243661.2 | c.231C>G | p.His77Gln | missense_variant | 3/3 | ||
NUDT7 | NM_001243657.2 | c.484C>G | p.Gln162Glu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT7 | ENST00000268533.9 | c.390C>G | p.His130Gln | missense_variant | 4/4 | 1 | NM_001105663.3 | P1 | |
ENST00000563690.1 | n.645G>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000117 AC: 29AN: 248722Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134986
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461002Hom.: 4 Cov.: 33 AF XY: 0.000120 AC XY: 87AN XY: 726830
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.390C>G (p.H130Q) alteration is located in exon 4 (coding exon 4) of the NUDT7 gene. This alteration results from a C to G substitution at nucleotide position 390, causing the histidine (H) at amino acid position 130 to be replaced by a glutamine (Q). 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