rs2117317
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142966.3(GREB1L):c.710-67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 1,324,292 control chromosomes in the GnomAD database, including 140,375 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 0.54 ( 24545 hom., cov: 32)
Exomes 𝑓: 0.44 ( 115830 hom. )
Consequence
GREB1L
NM_001142966.3 intron
NM_001142966.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.403
Genes affected
GREB1L (HGNC:31042): (GREB1 like retinoic acid receptor coactivator) Acts upstream of or within kidney development. Predicted to be integral component of membrane. Implicated in autosomal dominant nonsyndromic deafness and renal agenesis. [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 (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GREB1L | NM_001142966.3 | c.710-67C>T | intron_variant | Intron 6 of 32 | ENST00000424526.7 | NP_001136438.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.543 AC: 82538AN: 151918Hom.: 24497 Cov.: 32
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GnomAD4 exome AF: 0.436 AC: 511240AN: 1172256Hom.: 115830 AF XY: 0.437 AC XY: 255578AN XY: 584366
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GnomAD4 genome AF: 0.544 AC: 82648AN: 152036Hom.: 24545 Cov.: 32 AF XY: 0.545 AC XY: 40520AN XY: 74312
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at