19-371249-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016585.5(SPMAP2):c.709G>A(p.Ala237Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,510,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016585.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THEG | ENST00000342640.9 | c.709G>A | p.Ala237Thr | missense_variant | Exon 6 of 8 | 1 | NM_016585.5 | ENSP00000340088.3 | ||
THEG | ENST00000346878.3 | c.637G>A | p.Ala213Thr | missense_variant | Exon 5 of 7 | 2 | ENSP00000264820.3 | |||
THEG | ENST00000530711.3 | c.86+3050G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000475782.2 | ||||
THEG | ENST00000528213.1 | n.516G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000267 AC: 5AN: 187154Hom.: 0 AF XY: 0.0000296 AC XY: 3AN XY: 101318
GnomAD4 exome AF: 0.0000199 AC: 27AN: 1357906Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 18AN XY: 669792
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at