1-24364404-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_198174.3(GRHL3):c.*33C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0338 in 1,506,808 control chromosomes in the GnomAD database, including 1,844 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.064 ( 596 hom., cov: 33)
Exomes 𝑓: 0.030 ( 1248 hom. )
Consequence
GRHL3
NM_198174.3 3_prime_UTR
NM_198174.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.47
Genes affected
STPG1 (HGNC:28070): (sperm tail PG-rich repeat containing 1) Involved in positive regulation of apoptotic process and positive regulation of mitochondrial membrane permeability involved in apoptotic process. Predicted to be located in mitochondrion and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
GRHL3 (HGNC:25839): (grainyhead like transcription factor 3) This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 1-24364404-C-T is Benign according to our data. Variant chr1-24364404-C-T is described in ClinVar as [Benign]. Clinvar id is 1264843.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0635 AC: 9668AN: 152168Hom.: 591 Cov.: 33
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GnomAD3 exomes AF: 0.0451 AC: 4909AN: 108922Hom.: 220 AF XY: 0.0482 AC XY: 2728AN XY: 56546
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GnomAD4 exome AF: 0.0304 AC: 41191AN: 1354524Hom.: 1248 Cov.: 31 AF XY: 0.0320 AC XY: 21258AN XY: 663574
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GnomAD4 genome AF: 0.0636 AC: 9687AN: 152284Hom.: 596 Cov.: 33 AF XY: 0.0646 AC XY: 4811AN XY: 74474
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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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