chr9-137087030-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016219.5(MAN1B1):c.31G>A(p.Ala11Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,602,316 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A11A) has been classified as Likely benign.
Frequency
Consequence
NM_016219.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.31G>A | p.Ala11Thr | missense_variant | 1/13 | ENST00000371589.9 | |
MAN1B1 | XM_006716945.5 | c.31G>A | p.Ala11Thr | missense_variant | 1/12 | ||
MAN1B1 | NR_045720.2 | n.46G>A | non_coding_transcript_exon_variant | 1/13 | |||
MAN1B1 | NR_045721.2 | n.46G>A | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.31G>A | p.Ala11Thr | missense_variant | 1/13 | 1 | NM_016219.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000806 AC: 18AN: 223462Hom.: 2 AF XY: 0.000107 AC XY: 13AN XY: 121574
GnomAD4 exome AF: 0.0000303 AC: 44AN: 1450044Hom.: 2 Cov.: 31 AF XY: 0.0000403 AC XY: 29AN XY: 720266
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74402
ClinVar
Submissions by phenotype
Rafiq syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at