rs220285
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004416.3(UMODL1):c.77-97C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 1,544,070 control chromosomes in the GnomAD database, including 279,276 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 0.57 ( 25114 hom., cov: 35)
Exomes 𝑓: 0.60 ( 254162 hom. )
Consequence
UMODL1
NM_001004416.3 intron
NM_001004416.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.38
Genes affected
UMODL1 (HGNC:12560): (uromodulin like 1) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in neutrophil migration. Predicted to act upstream of or within several processes, including adipose tissue development; cellular response to gonadotropin-releasing hormone; and regulation of ovarian follicle development. Predicted to be located in cytoplasm and external side of plasma membrane. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane; cell surface; and extracellular space. [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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMODL1 | NM_001004416.3 | c.77-97C>G | intron_variant | ENST00000408910.7 | |||
UMODL1 | NM_001199527.3 | c.-140-97C>G | intron_variant | ||||
UMODL1 | NM_001199528.4 | c.-140-97C>G | intron_variant | ||||
UMODL1 | NM_173568.4 | c.77-97C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMODL1 | ENST00000408910.7 | c.77-97C>G | intron_variant | 1 | NM_001004416.3 | P2 | |||
UMODL1 | ENST00000400424.6 | c.-140-97C>G | intron_variant | 1 | A2 | ||||
UMODL1 | ENST00000400427.5 | c.-140-97C>G | intron_variant | 1 | A2 | ||||
UMODL1 | ENST00000408989.6 | c.77-97C>G | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.567 AC: 86194AN: 152126Hom.: 25089 Cov.: 35
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GnomAD4 exome AF: 0.598 AC: 831694AN: 1391826Hom.: 254162 AF XY: 0.595 AC XY: 407905AN XY: 685608
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GnomAD4 genome ? AF: 0.567 AC: 86257AN: 152244Hom.: 25114 Cov.: 35 AF XY: 0.561 AC XY: 41730AN XY: 74446
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at