1-152213508-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001009931.3(HRNR):c.8121C>A(p.Tyr2707*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Y2707Y) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000099 ( 0 hom., cov: 12)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HRNR
NM_001009931.3 stop_gained
NM_001009931.3 stop_gained
Scores
2
5
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.349
Genes affected
HRNR (HGNC:20846): (hornerin) Predicted to enable calcium ion binding activity and transition metal ion binding activity. Involved in cell envelope organization and establishment of skin barrier. Located in cornified envelope; keratohyalin granule; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 100824Hom.: 0 Cov.: 12 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000159 AC: 2AN: 1257738Hom.: 0 Cov.: 30 AF XY: 0.00000159 AC XY: 1AN XY: 630732
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000992 AC: 1AN: 100824Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0AN XY: 47812
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
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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