rs10259199
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001302348.2(UMAD1):c.156+7538T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,856 control chromosomes in the GnomAD database, including 2,535 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 0.17 ( 2535 hom., cov: 32)
Consequence
UMAD1
NM_001302348.2 intron
NM_001302348.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.790
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMAD1 | NM_001302348.2 | c.156+7538T>C | intron_variant | ENST00000682710.1 | |||
UMAD1 | NM_001302349.2 | c.156+7538T>C | intron_variant | ||||
UMAD1 | NM_001302350.2 | c.51+7538T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMAD1 | ENST00000682710.1 | c.156+7538T>C | intron_variant | NM_001302348.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.172 AC: 26112AN: 151738Hom.: 2532 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.172 AC: 26127AN: 151856Hom.: 2535 Cov.: 32 AF XY: 0.174 AC XY: 12940AN XY: 74244
GnomAD4 genome
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26127
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32
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12940
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74244
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344
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at