8-101558785-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_024915.4(GRHL2):c.651C>T(p.Ser217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,614,042 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.012 ( 42 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 43 hom. )
Consequence
GRHL2
NM_024915.4 synonymous
NM_024915.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.286
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 8-101558785-C-T is Benign according to our data. Variant chr8-101558785-C-T is described in ClinVar as [Benign]. Clinvar id is 46220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.286 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0124 (1895/152264) while in subpopulation AFR AF= 0.0431 (1790/41542). AF 95% confidence interval is 0.0414. There are 42 homozygotes in gnomad4. There are 876 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 42 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.651C>T | p.Ser217= | synonymous_variant | 4/16 | ENST00000646743.1 | |
GRHL2 | NM_001330593.2 | c.603C>T | p.Ser201= | synonymous_variant | 4/16 | ||
GRHL2 | XM_011517306.4 | c.603C>T | p.Ser201= | synonymous_variant | 4/16 | ||
GRHL2 | XM_011517307.4 | c.651C>T | p.Ser217= | synonymous_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.651C>T | p.Ser217= | synonymous_variant | 4/16 | NM_024915.4 | P1 | ||
GRHL2 | ENST00000395927.1 | c.603C>T | p.Ser201= | synonymous_variant | 4/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1894AN: 152146Hom.: 42 Cov.: 32
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GnomAD3 exomes AF: 0.00313 AC: 785AN: 250408Hom.: 15 AF XY: 0.00229 AC XY: 310AN XY: 135576
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GnomAD4 exome AF: 0.00124 AC: 1813AN: 1461778Hom.: 43 Cov.: 33 AF XY: 0.00110 AC XY: 799AN XY: 727170
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2017 | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Ser217Ser in Exon 04 of GRHL2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 3.9% (145/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs34332949). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at