chr7-117222921-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The ENST00000265437.9(ST7):c.1699C>T(p.Arg567Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R567L) has been classified as Likely benign.
Frequency
Consequence
ENST00000265437.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST7 | NM_001369598.1 | c.1638+859C>T | intron_variant | ENST00000323984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.1638+859C>T | intron_variant | 5 | NM_001369598.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249040Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134812
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461848Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727226
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1699C>T (p.R567C) alteration is located in exon 16 (coding exon 16) of the ST7 gene. This alteration results from a C to T substitution at nucleotide position 1699, causing the arginine (R) at amino acid position 567 to be replaced by a cysteine (C). 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