chr16-77735895-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105663.3(NUDT7):c.257C>A(p.Ala86Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,640 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_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.257C>A | p.Ala86Glu | missense_variant | 3/4 | ENST00000268533.9 | |
NUDT7 | NM_001243657.2 | c.257C>A | p.Ala86Glu | missense_variant | 3/5 | ||
NUDT7 | NM_001243660.2 | c.303+388C>A | intron_variant | ||||
NUDT7 | NM_001243661.2 | c.190-5687C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUDT7 | ENST00000268533.9 | c.257C>A | p.Ala86Glu | missense_variant | 3/4 | 1 | NM_001105663.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249578Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135404
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461640Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727144
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.257C>A (p.A86E) alteration is located in exon 3 (coding exon 3) of the NUDT7 gene. This alteration results from a C to A substitution at nucleotide position 257, causing the alanine (A) at amino acid position 86 to be replaced by a glutamic acid (E). 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