NM_001039958.2:c.885G>C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001039958.2(MESP2):c.885G>C(p.Thr295Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,611,398 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T295T) has been classified as Likely benign.
Frequency
Consequence
NM_001039958.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MESP2 | ENST00000341735.5 | c.885G>C | p.Thr295Thr | synonymous_variant | Exon 1 of 2 | 1 | NM_001039958.2 | ENSP00000342392.3 | ||
MESP2 | ENST00000560219.2 | c.31-823G>C | intron_variant | Intron 2 of 2 | 1 | ENSP00000452998.1 | ||||
MESP2 | ENST00000558723.1 | n.39-823G>C | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000832 AC: 2AN: 240406Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132276
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459152Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 725696
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:1
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Spondylocostal dysostosis 2, autosomal recessive Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at