chr7-116953586-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001369598.1(ST7):āc.46A>Cā(p.Ile16Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,338,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001369598.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST7 | NM_001369598.1 | c.46A>C | p.Ile16Leu | missense_variant | 1/16 | ENST00000323984.8 | |
ST7-AS1 | NR_002330.1 | n.749T>G | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.46A>C | p.Ile16Leu | missense_variant | 1/16 | 5 | NM_001369598.1 | ||
ST7-AS1 | ENST00000456775.1 | n.749T>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.0000194 AC: 26AN: 1338396Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 12AN XY: 666892
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.46A>C (p.I16L) alteration is located in exon 1 (coding exon 1) of the ST7 gene. This alteration results from a A to C substitution at nucleotide position 46, causing the isoleucine (I) at amino acid position 16 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at