14-57594035-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001306087.2(SLC35F4):āc.193T>Cā(p.Ser65Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001306087.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35F4 | NM_001306087.2 | c.193T>C | p.Ser65Pro | missense_variant | 2/8 | ENST00000556826.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35F4 | ENST00000556826.6 | c.193T>C | p.Ser65Pro | missense_variant | 2/8 | 5 | NM_001306087.2 | P1 | |
ENST00000647916.1 | n.873-5965A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249084Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135132
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461626Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727096
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.193T>C (p.S65P) alteration is located in exon 2 (coding exon 2) of the SLC35F4 gene. This alteration results from a T to C substitution at nucleotide position 193, causing the serine (S) at amino acid position 65 to be replaced by a proline (P). 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