4-39556568-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_174921.3(SMIM14):c.127C>T(p.Pro43Ser) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000245 in 1,589,120 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174921.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMIM14 | NM_174921.3 | c.127C>T | p.Pro43Ser | missense_variant, splice_region_variant | Exon 4 of 5 | ENST00000295958.10 | NP_777581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000262 AC: 6AN: 228614Hom.: 0 AF XY: 0.0000404 AC XY: 5AN XY: 123874
GnomAD4 exome AF: 0.0000251 AC: 36AN: 1437070Hom.: 0 Cov.: 30 AF XY: 0.0000210 AC XY: 15AN XY: 714540
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.127C>T (p.P43S) alteration is located in exon 4 (coding exon 3) of the SMIM14 gene. This alteration results from a C to T substitution at nucleotide position 127, causing the proline (P) at amino acid position 43 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