8-101543444-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024915.4(GRHL2):c.216+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024915.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRHL2 | NM_024915.4 | c.216+8C>T | splice_region_variant, intron_variant | ENST00000646743.1 | NP_079191.2 | |||
GRHL2 | NM_001330593.2 | c.168+8C>T | splice_region_variant, intron_variant | NP_001317522.1 | ||||
GRHL2 | XM_011517306.4 | c.168+8C>T | splice_region_variant, intron_variant | XP_011515608.1 | ||||
GRHL2 | XM_011517307.4 | c.216+8C>T | splice_region_variant, intron_variant | XP_011515609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRHL2 | ENST00000646743.1 | c.216+8C>T | splice_region_variant, intron_variant | NM_024915.4 | ENSP00000495564.1 | |||||
GRHL2 | ENST00000472106.2 | n.552C>T | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
GRHL2 | ENST00000395927.1 | c.168+8C>T | splice_region_variant, intron_variant | 2 | ENSP00000379260.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250640Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135492
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461024Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726862
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | 216+8C>T in Intron 02 of GRHL2: This variant is not expected to have clinical si gnificance because it is not located within the conserved splice consensus seque nce and has been identified in 0.1% (3/3738) of African American chromosomes fro m a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washin gton.edu/EVS). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at