chr6-44254909-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_178148.4(SLC35B2):c.1096G>A(p.Val366Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,160 control chromosomes in the GnomAD database, including 4 homozygotes. 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_178148.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35B2 | NM_178148.4 | c.1096G>A | p.Val366Ile | missense_variant | 4/4 | ENST00000393812.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35B2 | ENST00000393812.4 | c.1096G>A | p.Val366Ile | missense_variant | 4/4 | 1 | NM_178148.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152166Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251328Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135840
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461876Hom.: 1 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727238
GnomAD4 genome AF: 0.000125 AC: 19AN: 152284Hom.: 3 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.1096G>A (p.V366I) alteration is located in exon 4 (coding exon 4) of the SLC35B2 gene. This alteration results from a G to A substitution at nucleotide position 1096, causing the valine (V) at amino acid position 366 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