chr9-96324157-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007001.3(SLC35D2):c.765G>A(p.Met255Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,518 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. M255T) has been classified as Uncertain significance.
Frequency
Consequence
NM_007001.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35D2 | NM_007001.3 | c.765G>A | p.Met255Ile | missense_variant | Exon 10 of 12 | ENST00000253270.13 | NP_008932.2 | |
SLC35D2 | NM_001286990.2 | c.501G>A | p.Met167Ile | missense_variant | Exon 7 of 9 | NP_001273919.1 | ||
SLC35D2 | NR_104627.2 | n.842G>A | non_coding_transcript_exon_variant | Exon 10 of 13 | ||||
SLC35D2-HSD17B3 | NR_182427.1 | n.842G>A | non_coding_transcript_exon_variant | Exon 10 of 26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC35D2 | ENST00000253270.13 | c.765G>A | p.Met255Ile | missense_variant | Exon 10 of 12 | 1 | NM_007001.3 | ENSP00000253270.7 | ||
ENSG00000285269 | ENST00000643789.1 | n.366G>A | non_coding_transcript_exon_variant | Exon 6 of 22 | ENSP00000494818.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461518Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727030
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.765G>A (p.M255I) alteration is located in exon 10 (coding exon 10) of the SLC35D2 gene. This alteration results from a G to A substitution at nucleotide position 765, causing the methionine (M) at amino acid position 255 to be replaced by an isoleucine (I). 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
Publications
No publications associated with this variant yet.