chr6-116110896-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152729.3(NT5DC1):c.304G>T(p.Ala102Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,614,036 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_152729.3 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 |
---|---|---|---|---|---|---|---|
NT5DC1 | NM_152729.3 | c.304G>T | p.Ala102Ser | missense_variant | 4/12 | ENST00000319550.9 | |
NT5DC1 | XM_006715378.4 | c.304G>T | p.Ala102Ser | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC1 | ENST00000319550.9 | c.304G>T | p.Ala102Ser | missense_variant | 4/12 | 1 | NM_152729.3 | P1 | |
NT5DC1 | ENST00000419791.3 | c.304G>T | p.Ala102Ser | missense_variant | 4/7 | 3 | |||
NT5DC1 | ENST00000417846.2 | n.45G>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251438Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135890
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.000157 AC XY: 114AN XY: 727216
GnomAD4 genome AF: 0.000125 AC: 19AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.304G>T (p.A102S) alteration is located in exon 4 (coding exon 4) of the NT5DC1 gene. This alteration results from a G to T substitution at nucleotide position 304, causing the alanine (A) at amino acid position 102 to be replaced by a serine (S). 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