chr8-101558775-G-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_024915.4(GRHL2):c.641G>A(p.Ser214Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,614,038 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 Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000083 ( 0 hom. )
Consequence
GRHL2
NM_024915.4 missense
NM_024915.4 missense
Scores
5
5
9
Clinical Significance
Conservation
PhyloP100: 8.84
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 -1 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.41768682).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.641G>A | p.Ser214Asn | missense_variant | Exon 4 of 16 | ENST00000646743.1 | NP_079191.2 | |
GRHL2 | NM_001330593.2 | c.593G>A | p.Ser198Asn | missense_variant | Exon 4 of 16 | NP_001317522.1 | ||
GRHL2 | XM_011517306.4 | c.593G>A | p.Ser198Asn | missense_variant | Exon 4 of 16 | XP_011515608.1 | ||
GRHL2 | XM_011517307.4 | c.641G>A | p.Ser214Asn | missense_variant | Exon 4 of 16 | XP_011515609.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000678 AC: 17AN: 250670Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135658
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GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461830Hom.: 0 Cov.: 33 AF XY: 0.0000880 AC XY: 64AN XY: 727208
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GnomAD4 genome AF: 0.0000985 AC: 15AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74360
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 19, 2024 | This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 214 of the GRHL2 protein (p.Ser214Asn). This variant is present in population databases (rs199931364, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with GRHL2-related conditions. ClinVar contains an entry for this variant (Variation ID: 228733). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt GRHL2 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2024 | In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 11, 2018 | The p.Ser214Asn variant in GRHL2 has been reported in 1 individual with mild sen sorineural hearing loss (LMM data). This variant has been identified in 14/12629 2 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad .broadinstitute.org; dbSNP rs199931364). Computational prediction tools and cons ervation analysis suggest that the p.Ser214Asn variant may impact the protein, t hough this information is not predictive enough to determine pathogenicity. In s ummary, the clinical significance of the p.Ser214Asn variant is uncertain. ACMG/ AMP Criteria applied: PM2_Supporting, PP3 - |
Corneal dystrophy, posterior polymorphous, 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Aug 05, 2022 | ACMG classification criteria: BP4 supporting - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Uncertain
D;.;D
Sift4G
Uncertain
D;.;D
Polyphen
D;D;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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