chr9-137087035-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_016219.5(MAN1B1):āc.36C>Gā(p.Leu12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000948 in 1,603,066 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.36C>G | p.Leu12= | synonymous_variant | 1/13 | ENST00000371589.9 | |
MAN1B1 | XM_006716945.5 | c.36C>G | p.Leu12= | synonymous_variant | 1/12 | ||
MAN1B1 | NR_045720.2 | n.51C>G | non_coding_transcript_exon_variant | 1/13 | |||
MAN1B1 | NR_045721.2 | n.51C>G | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.36C>G | 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: 0.000214 AC: 48AN: 224152Hom.: 0 AF XY: 0.000287 AC XY: 35AN XY: 121994
GnomAD4 exome AF: 0.000100 AC: 145AN: 1450706Hom.: 1 Cov.: 31 AF XY: 0.000137 AC XY: 99AN XY: 720672
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152360Hom.: 0 Cov.: 34 AF XY: 0.0000805 AC XY: 6AN XY: 74506
ClinVar
Submissions by phenotype
Rafiq syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at