chr2-230470015-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080391.2(SP100):c.1346G>T(p.Arg449Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,611,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080391.2 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SP100 | NM_001080391.2 | c.1346G>T | p.Arg449Leu | missense_variant, splice_region_variant | 15/29 | ENST00000340126.9 | |
LOC101928816 | XR_427235.4 | n.472-26650C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SP100 | ENST00000340126.9 | c.1346G>T | p.Arg449Leu | missense_variant, splice_region_variant | 15/29 | 1 | NM_001080391.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247494Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133772
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1458914Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 725638
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.1346G>T (p.R449L) alteration is located in exon 15 (coding exon 15) of the SP100 gene. This alteration results from a G to T substitution at nucleotide position 1346, causing the arginine (R) at amino acid position 449 to be replaced by a leucine (L). 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