chr9-137087064-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016219.5(MAN1B1):c.65C>T(p.Pro22Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,603,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016219.5 missense
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 |
---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.65C>T | p.Pro22Leu | missense_variant | 1/13 | ENST00000371589.9 | |
MAN1B1 | XM_006716945.5 | c.65C>T | p.Pro22Leu | missense_variant | 1/12 | ||
MAN1B1 | NR_045720.2 | n.80C>T | non_coding_transcript_exon_variant | 1/13 | |||
MAN1B1 | NR_045721.2 | n.80C>T | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.65C>T | p.Pro22Leu | missense_variant | 1/13 | 1 | NM_016219.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152264Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000135 AC: 3AN: 222422Hom.: 0 AF XY: 0.0000165 AC XY: 2AN XY: 121442
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1451344Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 721082
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152264Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74398
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.65C>T (p.P22L) alteration is located in exon 1 (coding exon 1) of the MAN1B1 gene. This alteration results from a C to T substitution at nucleotide position 65, causing the proline (P) at amino acid position 22 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