rs1146298
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006699.5(MAN1A2):c.302+4800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,670 control chromosomes in the GnomAD database, including 44,922 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.77 ( 44922 hom., cov: 29)
Consequence
MAN1A2
NM_006699.5 intron
NM_006699.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.383
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1A2 | NM_006699.5 | c.302+4800G>A | intron_variant | ENST00000356554.7 | |||
MAN1A2 | XM_006710302.4 | c.302+4800G>A | intron_variant | ||||
MAN1A2 | XM_011540536.4 | c.302+4800G>A | intron_variant | ||||
MAN1A2 | XM_017000115.2 | c.302+4800G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1A2 | ENST00000356554.7 | c.302+4800G>A | intron_variant | 1 | NM_006699.5 | P1 | |||
MAN1A2 | ENST00000482811.1 | n.543+4800G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.768 AC: 116402AN: 151552Hom.: 44882 Cov.: 29
GnomAD3 genomes
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116402
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.768 AC: 116500AN: 151670Hom.: 44922 Cov.: 29 AF XY: 0.766 AC XY: 56731AN XY: 74106
GnomAD4 genome
?
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116500
AN:
151670
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29
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56731
AN XY:
74106
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Asia WGS
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2536
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at