X-21843225-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_015884.4(MBTPS2):āc.131G>Cā(p.Ser44Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,095,503 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_015884.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBTPS2 | NM_015884.4 | c.131G>C | p.Ser44Thr | missense_variant | 2/11 | ENST00000379484.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBTPS2 | ENST00000379484.10 | c.131G>C | p.Ser44Thr | missense_variant | 2/11 | 1 | NM_015884.4 | P1 | |
MBTPS2 | ENST00000365779.2 | c.131G>C | p.Ser44Thr | missense_variant | 2/7 | 1 | |||
MBTPS2 | ENST00000465888.1 | n.230G>C | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183511Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67943
GnomAD4 exome AF: 0.0000110 AC: 12AN: 1095503Hom.: 0 Cov.: 29 AF XY: 0.00000554 AC XY: 2AN XY: 360899
GnomAD4 genome Cov.: 24
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at