chr8-101543073-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024915.4(GRHL2):c.21-168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,188 control chromosomes in the GnomAD database, including 16,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.42 ( 16100 hom., cov: 33)
Consequence
GRHL2
NM_024915.4 intron
NM_024915.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0850
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 8-101543073-A-G is Benign according to our data. Variant chr8-101543073-A-G is described in ClinVar as [Benign]. Clinvar id is 1286039.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.21-168A>G | intron_variant | ENST00000646743.1 | |||
GRHL2 | NM_001330593.2 | c.-28-168A>G | intron_variant | ||||
GRHL2 | XM_011517306.4 | c.-28-168A>G | intron_variant | ||||
GRHL2 | XM_011517307.4 | c.21-168A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.21-168A>G | intron_variant | NM_024915.4 | P1 | ||||
GRHL2 | ENST00000472106.2 | n.349-168A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
GRHL2 | ENST00000395927.1 | c.-28-168A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.424 AC: 64498AN: 152070Hom.: 16102 Cov.: 33
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.424 AC: 64510AN: 152188Hom.: 16100 Cov.: 33 AF XY: 0.424 AC XY: 31559AN XY: 74394
GnomAD4 genome
?
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
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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