8-101492313-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NR_186783.1(GRHL2-DT):n.257-8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 188,778 control chromosomes in the GnomAD database, including 88,413 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.97 ( 71128 hom., cov: 34)
Exomes 𝑓: 0.97 ( 17285 hom. )
Consequence
GRHL2-DT
NR_186783.1 splice_region, intron
NR_186783.1 splice_region, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.184
Genes affected
GRHL2-DT (HGNC:55466): (GRHL2 divergent transcript)
GRHL2 (HGNC:2799): (grainyhead like transcription factor 2) The protein encoded by this gene is a transcription factor that can act as a homodimer or as a heterodimer with either GRHL1 or GRHL3. Defects in this gene are a cause of non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28).[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 8-101492313-C-T is Benign according to our data. Variant chr8-101492313-C-T is described in ClinVar as [Benign]. Clinvar id is 1222504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.966 AC: 146999AN: 152230Hom.: 71100 Cov.: 34
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GnomAD4 exome AF: 0.973 AC: 35459AN: 36430Hom.: 17285 AF XY: 0.973 AC XY: 18357AN XY: 18874
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GnomAD4 genome AF: 0.965 AC: 147082AN: 152348Hom.: 71128 Cov.: 34 AF XY: 0.964 AC XY: 71840AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at