rs201918928
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016219.5(MAN1B1):c.1255-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,611,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016219.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.1255-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000371589.9 | |||
MAN1B1 | XM_006716945.5 | c.1255-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MAN1B1 | NR_045720.2 | n.1270-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
MAN1B1 | NR_045721.2 | n.1401-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.1255-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016219.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247070Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134324
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1459484Hom.: 0 Cov.: 32 AF XY: 0.0000152 AC XY: 11AN XY: 726070
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152344Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74478
ClinVar
Submissions by phenotype
Rafiq syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at