17-50112924-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.1223G>A(p.Arg408Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,607,670 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001257359.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.1223G>A | p.Arg408Gln | missense_variant | Exon 10 of 10 | ENST00000330175.9 | NP_001244288.1 | |
SAMD14 | NM_174920.4 | c.1307G>A | p.Arg436Gln | missense_variant | Exon 11 of 11 | NP_777580.1 | ||
SAMD14 | XM_017024322.3 | c.1472G>A | p.Arg491Gln | missense_variant | Exon 9 of 9 | XP_016879811.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000567 AC: 14AN: 246720Hom.: 1 AF XY: 0.0000672 AC XY: 9AN XY: 133838
GnomAD4 exome AF: 0.000120 AC: 175AN: 1455446Hom.: 1 Cov.: 31 AF XY: 0.000115 AC XY: 83AN XY: 724342
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1307G>A (p.R436Q) 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 1307, causing the arginine (R) at amino acid position 436 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