rs727504472
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_024915.4(GRHL2):c.285-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00786 in 1,613,572 control chromosomes in the GnomAD database, including 73 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0057 ( 3 hom., cov: 31)
Exomes 𝑓: 0.0081 ( 70 hom. )
Consequence
GRHL2
NM_024915.4 intron
NM_024915.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.284
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 Benign. Variant got -16 ACMG points.
BP6
Variant 8-101558399-CG-C is Benign according to our data. Variant chr8-101558399-CG-C is described in ClinVar as [Benign]. Clinvar id is 178828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00568 (865/152176) while in subpopulation NFE AF= 0.00906 (616/68010). AF 95% confidence interval is 0.00847. There are 3 homozygotes in gnomad4. There are 413 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.285-14del | intron_variant | ENST00000646743.1 | |||
GRHL2 | NM_001330593.2 | c.237-14del | intron_variant | ||||
GRHL2 | XM_011517306.4 | c.237-14del | intron_variant | ||||
GRHL2 | XM_011517307.4 | c.285-14del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.285-14del | intron_variant | NM_024915.4 | P1 | ||||
GRHL2 | ENST00000395927.1 | c.237-14del | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00570 AC: 866AN: 152058Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.00529 AC: 1328AN: 251216Hom.: 6 AF XY: 0.00509 AC XY: 691AN XY: 135814
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GnomAD4 exome AF: 0.00809 AC: 11824AN: 1461396Hom.: 70 Cov.: 32 AF XY: 0.00777 AC XY: 5650AN XY: 727032
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GnomAD4 genome AF: 0.00568 AC: 865AN: 152176Hom.: 3 Cov.: 31 AF XY: 0.00555 AC XY: 413AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 11, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 04, 2016 | c.285-14delG in intron 3 of GRHL2: This variant is not expected to have clinical significance because it has been identified in 0.74% (491/66712) of European ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs559133364). - |
Computational scores
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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