chr16-1078918-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001172560.3(SSTR5):c.50C>T(p.Pro17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000053 in 1,603,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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. P17R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001172560.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR5 | NM_001172560.3 | c.50C>T | p.Pro17Leu | missense_variant | 2/2 | ENST00000689027.1 | |
SSTR5 | NM_001053.4 | c.50C>T | p.Pro17Leu | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR5 | ENST00000689027.1 | c.50C>T | p.Pro17Leu | missense_variant | 2/2 | NM_001172560.3 | P1 | ||
SSTR5 | ENST00000293897.7 | c.50C>T | p.Pro17Leu | missense_variant | 1/1 | P1 | |||
SSTR5 | ENST00000711615.1 | c.50C>T | p.Pro17Leu | missense_variant | 2/2 | P1 | |||
SSTR5 | ENST00000711616.1 | c.50C>T | p.Pro17Leu | missense_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000662 AC: 15AN: 226584Hom.: 0 AF XY: 0.0000401 AC XY: 5AN XY: 124786
GnomAD4 exome AF: 0.0000379 AC: 55AN: 1451588Hom.: 0 Cov.: 29 AF XY: 0.0000305 AC XY: 22AN XY: 721886
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.50C>T (p.P17L) alteration is located in exon 1 (coding exon 1) of the SSTR5 gene. This alteration results from a C to T substitution at nucleotide position 50, causing the proline (P) at amino acid position 17 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