rs1554579878
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_024915.4(GRHL2):c.20+544G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
GRHL2
NM_024915.4 intron
NM_024915.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.04
Genes affected
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 8-101493333-G-T is Pathogenic according to our data. Variant chr8-101493333-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 489403.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr8-101493333-G-T is described in Lovd as [Pathogenic].
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.20+544G>T | intron_variant | ENST00000646743.1 | |||
GRHL2 | NM_001330593.2 | c.-29+484G>T | intron_variant | ||||
GRHL2 | XM_011517306.4 | c.-29+747G>T | intron_variant | ||||
GRHL2 | XM_011517307.4 | c.20+544G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.20+544G>T | intron_variant | NM_024915.4 | P1 | ||||
GRHL2 | ENST00000472106.2 | n.348+544G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
GRHL2 | ENST00000395927.1 | c.-29+484G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Corneal dystrophy, posterior polymorphous, 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 12, 2022 | - - |
Corneal dystrophy Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Hardcastle Lab, UCL Institute of Ophthalmology | Feb 02, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at