chr14-57566487-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001306087.2(SLC35F4):c.1204C>T(p.Pro402Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,594,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001306087.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35F4 | NM_001306087.2 | c.1204C>T | p.Pro402Ser | missense_variant | 7/8 | ENST00000556826.6 | |
LOC105370519 | XR_007064194.1 | n.2863+492G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35F4 | ENST00000556826.6 | c.1204C>T | p.Pro402Ser | missense_variant | 7/8 | 5 | NM_001306087.2 | P1 | |
SLC35F4 | ENST00000554729.5 | c.835C>T | p.Pro279Ser | missense_variant | 7/8 | 1 | |||
SLC35F4 | ENST00000557254.5 | c.*565C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 1 | ||||
SLC35F4 | ENST00000339762.10 | c.1312C>T | p.Pro438Ser | missense_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000146 AC: 32AN: 219930Hom.: 0 AF XY: 0.000161 AC XY: 19AN XY: 117904
GnomAD4 exome AF: 0.000169 AC: 243AN: 1441954Hom.: 0 Cov.: 30 AF XY: 0.000171 AC XY: 122AN XY: 714828
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.1201C>T (p.P401S) alteration is located in exon 7 (coding exon 7) of the SLC35F4 gene. This alteration results from a C to T substitution at nucleotide position 1201, causing the proline (P) at amino acid position 401 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