chr7-117170983-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001369598.1(ST7):c.1078+7T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,566,746 control chromosomes in the GnomAD database, including 37,147 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 (★).
Frequency
Consequence
NM_001369598.1 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST7 | NM_001369598.1 | c.1078+7T>C | splice_region_variant, intron_variant | ENST00000323984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.1078+7T>C | splice_region_variant, intron_variant | 5 | NM_001369598.1 |
Frequencies
GnomAD3 genomes ? AF: 0.277 AC: 42022AN: 151828Hom.: 7010 Cov.: 31
GnomAD3 exomes AF: 0.219 AC: 52460AN: 239194Hom.: 6508 AF XY: 0.211 AC XY: 27274AN XY: 129372
GnomAD4 exome AF: 0.199 AC: 282176AN: 1414800Hom.: 30112 Cov.: 22 AF XY: 0.197 AC XY: 139269AN XY: 705262
GnomAD4 genome ? AF: 0.277 AC: 42099AN: 151946Hom.: 7035 Cov.: 31 AF XY: 0.272 AC XY: 20178AN XY: 74250
ClinVar
Submissions by phenotype
ST7-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at