chr17-50112936-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001257359.2(SAMD14):c.1211G>A(p.Arg404Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,608,882 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R404W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001257359.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD14 | NM_001257359.2 | c.1211G>A | p.Arg404Gln | missense_variant | Exon 10 of 10 | ENST00000330175.9 | NP_001244288.1 | |
SAMD14 | NM_174920.4 | c.1295G>A | p.Arg432Gln | missense_variant | Exon 11 of 11 | NP_777580.1 | ||
SAMD14 | XM_017024322.3 | c.1460G>A | p.Arg487Gln | missense_variant | Exon 9 of 9 | XP_016879811.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247656Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134258
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1456656Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 724926
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1295G>A (p.R432Q) alteration is located in exon 11 (coding exon 10) of the SAMD14 gene. This alteration results from a G to A substitution at nucleotide position 1295, causing the arginine (R) at amino acid position 432 to be replaced by a glutamine (Q). 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