rs138628340
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_024915.4(GRHL2):c.849C>T(p.Thr283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,614,044 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: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
GRHL2
NM_024915.4 synonymous
NM_024915.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.80
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 8-101573782-C-T is Benign according to our data. Variant chr8-101573782-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 504592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.8 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.849C>T | p.Thr283= | synonymous_variant | 6/16 | ENST00000646743.1 | |
GRHL2 | NM_001330593.2 | c.801C>T | p.Thr267= | synonymous_variant | 6/16 | ||
GRHL2 | XM_011517306.4 | c.801C>T | p.Thr267= | synonymous_variant | 6/16 | ||
GRHL2 | XM_011517307.4 | c.849C>T | p.Thr283= | synonymous_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.849C>T | p.Thr283= | synonymous_variant | 6/16 | NM_024915.4 | P1 | ||
GRHL2 | ENST00000395927.1 | c.801C>T | p.Thr267= | synonymous_variant | 6/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152158Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251470Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135908
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GnomAD4 exome AF: 0.000137 AC: 200AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.000118 AC XY: 86AN XY: 727244
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 24, 2017 | p.Thr283Thr in exon 06 of GRHL2: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 5/66688 European ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs138628340). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 23, 2022 | - - |
Computational scores
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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