2-230467165-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080391.2(SP100):c.1241C>T(p.Ala414Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,613,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080391.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SP100 | NM_001080391.2 | c.1241C>T | p.Ala414Val | missense_variant | 13/29 | ENST00000340126.9 | |
LOC101928816 | XR_427235.4 | n.472-23800G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SP100 | ENST00000340126.9 | c.1241C>T | p.Ala414Val | missense_variant | 13/29 | 1 | NM_001080391.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000267 AC: 67AN: 251192Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135748
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461568Hom.: 0 Cov.: 30 AF XY: 0.000105 AC XY: 76AN XY: 727098
GnomAD4 genome AF: 0.000197 AC: 30AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1241C>T (p.A414V) alteration is located in exon 13 (coding exon 13) of the SP100 gene. This alteration results from a C to T substitution at nucleotide position 1241, causing the alanine (A) at amino acid position 414 to be replaced by a valine (V). 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