rs10955255
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024915.4(GRHL2):c.21-19064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,066 control chromosomes in the GnomAD database, including 17,570 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 17570 hom., cov: 32)
Consequence
GRHL2
NM_024915.4 intron
NM_024915.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.298
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.21-19064A>G | intron_variant | ENST00000646743.1 | |||
GRHL2 | NM_001330593.2 | c.-28-19064A>G | intron_variant | ||||
GRHL2 | XM_011517306.4 | c.-28-19064A>G | intron_variant | ||||
GRHL2 | XM_011517307.4 | c.21-19064A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.21-19064A>G | intron_variant | NM_024915.4 | P1 | ||||
GRHL2 | ENST00000472106.2 | n.349-19064A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
GRHL2 | ENST00000395927.1 | c.-28-19064A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.449 AC: 68183AN: 151948Hom.: 17573 Cov.: 32
GnomAD3 genomes
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151948
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.448 AC: 68196AN: 152066Hom.: 17570 Cov.: 32 AF XY: 0.448 AC XY: 33280AN XY: 74346
GnomAD4 genome
?
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68196
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32
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33280
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74346
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1010
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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