chr7-134309384-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032826.5(SLC35B4):c.173C>T(p.Pro58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000453 in 1,608,706 control chromosomes in the GnomAD database, including 1 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_032826.5 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 |
---|---|---|---|---|---|---|---|
SLC35B4 | NM_032826.5 | c.173C>T | p.Pro58Leu | missense_variant | 2/10 | ENST00000378509.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35B4 | ENST00000378509.9 | c.173C>T | p.Pro58Leu | missense_variant | 2/10 | 1 | NM_032826.5 | P1 | |
SLC35B4 | ENST00000470969.2 | c.173C>T | p.Pro58Leu | missense_variant | 2/8 | 1 | |||
SLC35B4 | ENST00000416907.5 | c.173C>T | p.Pro58Leu | missense_variant, NMD_transcript_variant | 2/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000348 AC: 53AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000335 AC: 82AN: 245036Hom.: 0 AF XY: 0.000310 AC XY: 41AN XY: 132462
GnomAD4 exome AF: 0.000464 AC: 676AN: 1456470Hom.: 1 Cov.: 30 AF XY: 0.000449 AC XY: 325AN XY: 724376
GnomAD4 genome ? AF: 0.000348 AC: 53AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.173C>T (p.P58L) alteration is located in exon 2 (coding exon 2) of the SLC35B4 gene. This alteration results from a C to T substitution at nucleotide position 173, causing the proline (P) at amino acid position 58 to be replaced by a leucine (L). 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