7-22976212-T-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The ENST00000432176.7(HYCC1):āc.624A>Gā(p.Ser208=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,595,058 control chromosomes in the GnomAD database, including 99,736 homozygotes. 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 Benign (ā ā ).
Frequency
Consequence
ENST00000432176.7 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HYCC1 | NM_032581.4 | c.624A>G | p.Ser208= | splice_region_variant, synonymous_variant | 7/11 | ENST00000432176.7 | NP_115970.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYCC1 | ENST00000432176.7 | c.624A>G | p.Ser208= | splice_region_variant, synonymous_variant | 7/11 | 1 | NM_032581.4 | ENSP00000403396 |
Frequencies
GnomAD3 genomes AF: 0.353 AC: 53611AN: 151996Hom.: 9502 Cov.: 32
GnomAD3 exomes AF: 0.370 AC: 92045AN: 248962Hom.: 17338 AF XY: 0.368 AC XY: 49690AN XY: 134916
GnomAD4 exome AF: 0.351 AC: 506122AN: 1442944Hom.: 90225 Cov.: 29 AF XY: 0.351 AC XY: 252215AN XY: 718942
GnomAD4 genome AF: 0.353 AC: 53654AN: 152114Hom.: 9511 Cov.: 32 AF XY: 0.353 AC XY: 26219AN XY: 74376
ClinVar
Submissions by phenotype
Hypomyelination and Congenital Cataract Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at