chr9-137087035-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_016219.5(MAN1B1):c.36C>T(p.Leu12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000568 in 1,602,948 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. L12L) has been classified as Likely benign.
Frequency
Consequence
NM_016219.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.36C>T | p.Leu12= | synonymous_variant | 1/13 | ENST00000371589.9 | |
MAN1B1 | XM_006716945.5 | c.36C>T | p.Leu12= | synonymous_variant | 1/12 | ||
MAN1B1 | NR_045720.2 | n.51C>T | non_coding_transcript_exon_variant | 1/13 | |||
MAN1B1 | NR_045721.2 | n.51C>T | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.36C>T | p.Leu12= | synonymous_variant | 1/13 | 1 | NM_016219.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000357 AC: 8AN: 224152Hom.: 0 AF XY: 0.0000492 AC XY: 6AN XY: 121994
GnomAD4 exome AF: 0.0000579 AC: 84AN: 1450706Hom.: 0 Cov.: 31 AF XY: 0.0000555 AC XY: 40AN XY: 720672
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
Rafiq syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 17, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2017 | 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