rs2057931
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001302348.2(UMAD1):c.-63-3199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,986 control chromosomes in the GnomAD database, including 25,916 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 0.58 ( 25916 hom., cov: 32)
Consequence
UMAD1
NM_001302348.2 intron
NM_001302348.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0140
Genes affected
UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)
RPA3 (HGNC:10291): (replication protein A3) Enables damaged DNA binding activity and single-stranded DNA binding activity. Involved in DNA repair and DNA replication. Part of DNA replication factor A complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMAD1 | NM_001302348.2 | c.-63-3199C>T | intron_variant | ENST00000682710.1 | |||
RPA3 | NM_002947.5 | c.-758+15720G>A | intron_variant | ENST00000223129.8 | |||
UMAD1 | NM_001302349.2 | c.-56-3206C>T | intron_variant | ||||
UMAD1 | NM_001302350.2 | c.-275-3199C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPA3 | ENST00000223129.8 | c.-758+15720G>A | intron_variant | 1 | NM_002947.5 | P1 | |||
UMAD1 | ENST00000682710.1 | c.-63-3199C>T | intron_variant | NM_001302348.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.581 AC: 88260AN: 151868Hom.: 25899 Cov.: 32
GnomAD3 genomes
?
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88260
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151868
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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: 0.581 AC: 88312AN: 151986Hom.: 25916 Cov.: 32 AF XY: 0.584 AC XY: 43382AN XY: 74288
GnomAD4 genome
?
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88312
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151986
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32
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43382
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74288
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2186
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
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