1-152214975-C-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001009931.3(HRNR):āc.6654G>Cā(p.Ser2218Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000069 ( 0 hom., cov: 37)
Exomes š: 0.000014 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HRNR
NM_001009931.3 synonymous
NM_001009931.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
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 Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 1-152214975-C-G is Benign according to our data. Variant chr1-152214975-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3770869.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 144228Hom.: 0 Cov.: 37 FAILED QC
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GnomAD3 exomes AF: 0.0000252 AC: 2AN: 79386Hom.: 0 AF XY: 0.0000518 AC XY: 2AN XY: 38600
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000145 AC: 21AN: 1449422Hom.: 0 Cov.: 119 AF XY: 0.0000139 AC XY: 10AN XY: 721200
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000693 AC: 1AN: 144228Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 70404
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
HRNR: BP4, BP7 -
Computational scores
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Name
Calibrated prediction
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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