9-76503468-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001490.5(GCNT1):c.1087G>A(p.Val363Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,054 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_001490.5 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 |
---|---|---|---|---|---|---|---|
GCNT1 | NM_001490.5 | c.1087G>A | p.Val363Ile | missense_variant | 4/4 | ENST00000376730.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCNT1 | ENST00000376730.5 | c.1087G>A | p.Val363Ile | missense_variant | 4/4 | 1 | NM_001490.5 | P1 | |
GCNT1 | ENST00000442371.5 | c.1087G>A | p.Val363Ile | missense_variant | 3/3 | 1 | P1 | ||
GCNT1 | ENST00000444201.6 | c.1087G>A | p.Val363Ile | missense_variant | 3/3 | 1 | P1 | ||
GCNT1 | ENST00000648797.1 | n.142-12060G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152170Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461884Hom.: 0 Cov.: 34 AF XY: 0.00000550 AC XY: 4AN XY: 727242
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74330
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at