7-117222949-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The ENST00000265437.9(ST7):c.1727C>T(p.Pro576Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,613,822 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
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+887C>T | intron_variant | ENST00000323984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST7 | ENST00000323984.8 | c.1638+887C>T | intron_variant | 5 | NM_001369598.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000133 AC: 33AN: 249024Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134802
GnomAD4 exome AF: 0.0000924 AC: 135AN: 1461614Hom.: 2 Cov.: 30 AF XY: 0.0000880 AC XY: 64AN XY: 727146
GnomAD4 genome ? AF: 0.000355 AC: 54AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.1727C>T (p.P576L) 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 1727, causing the proline (P) at amino acid position 576 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