6-118314136-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001029858.4(SLC35F1):c.1111C>T(p.Arg371Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,614,060 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. R371H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001029858.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35F1 | NM_001029858.4 | c.1111C>T | p.Arg371Cys | missense_variant | 8/8 | ENST00000360388.9 | |
SLC35F1 | NM_001415931.1 | c.1111C>T | p.Arg371Cys | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35F1 | ENST00000360388.9 | c.1111C>T | p.Arg371Cys | missense_variant | 8/8 | 1 | NM_001029858.4 | A2 | |
SLC35F1 | ENST00000621341.1 | c.934C>T | p.Arg312Cys | missense_variant | 7/7 | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251490Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727244
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.1111C>T (p.R371C) alteration is located in exon 8 (coding exon 8) of the SLC35F1 gene. This alteration results from a C to T substitution at nucleotide position 1111, causing the arginine (R) at amino acid position 371 to be replaced by a cysteine (C). 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