7-117222070-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001369598.1(ST7):c.1638+8T>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 0.000297 in 1,603,394 control chromosomes in the GnomAD database, including 1 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
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST7 | NM_001369598.1 | c.1638+8T>C | splice_region_variant, intron_variant | ENST00000323984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.1638+8T>C | splice_region_variant, intron_variant | 5 | NM_001369598.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00165 AC: 251AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000419 AC: 100AN: 238666Hom.: 0 AF XY: 0.000271 AC XY: 35AN XY: 129146
GnomAD4 exome AF: 0.000155 AC: 225AN: 1451092Hom.: 1 Cov.: 30 AF XY: 0.000133 AC XY: 96AN XY: 721622
GnomAD4 genome ? AF: 0.00165 AC: 251AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at