chr16-77722605-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105663.3(NUDT7):c.23A>T(p.Glu8Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000176 in 1,594,614 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_001105663.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUDT7 | NM_001105663.3 | c.23A>T | p.Glu8Val | missense_variant | 1/4 | ENST00000268533.9 | |
NUDT7 | NM_001243660.2 | c.23A>T | p.Glu8Val | missense_variant | 1/4 | ||
NUDT7 | NM_001243661.2 | c.23A>T | p.Glu8Val | missense_variant | 1/3 | ||
NUDT7 | NM_001243657.2 | c.23A>T | p.Glu8Val | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT7 | ENST00000268533.9 | c.23A>T | p.Glu8Val | missense_variant | 1/4 | 1 | NM_001105663.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000139 AC: 3AN: 216224Hom.: 0 AF XY: 0.0000171 AC XY: 2AN XY: 117246
GnomAD4 exome AF: 0.00000971 AC: 14AN: 1442302Hom.: 0 Cov.: 31 AF XY: 0.00000559 AC XY: 4AN XY: 715546
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152312Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.23A>T (p.E8V) alteration is located in exon 1 (coding exon 1) of the NUDT7 gene. This alteration results from a A to T substitution at nucleotide position 23, causing the glutamic acid (E) at amino acid position 8 to be replaced by a valine (V). 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