8-101492747-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_024915.4(GRHL2):c.-23G>C variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00000274 in 1,460,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
GRHL2
NM_024915.4 5_prime_UTR
NM_024915.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.13
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 8-101492747-G-C is Benign according to our data. Variant chr8-101492747-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 515261.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.-23G>C | 5_prime_UTR_variant | 1/16 | ENST00000646743.1 | ||
GRHL2 | NM_001330593.2 | c.-131G>C | 5_prime_UTR_variant | 1/16 | |||
GRHL2 | XM_011517307.4 | c.-23G>C | 5_prime_UTR_variant | 1/16 | |||
GRHL2 | XM_011517306.4 | c.-29+161G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.-23G>C | 5_prime_UTR_variant | 1/16 | NM_024915.4 | P1 | |||
GRHL2 | ENST00000472106.2 | n.306G>C | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
GRHL2 | ENST00000521085.1 | c.-23G>C | 5_prime_UTR_variant | 2/2 | 3 | ||||
GRHL2 | ENST00000395927.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249050Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134826
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460586Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726714
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GnomAD4 genome ? Cov.: 32
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32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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