chr16-1078972-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001172560.3(SSTR5):c.104C>T(p.Ser35Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,591,710 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 (★).
Frequency
Consequence
NM_001172560.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR5 | NM_001172560.3 | c.104C>T | p.Ser35Leu | missense_variant | 2/2 | ENST00000689027.1 | |
SSTR5 | NM_001053.4 | c.104C>T | p.Ser35Leu | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR5 | ENST00000689027.1 | c.104C>T | p.Ser35Leu | missense_variant | 2/2 | NM_001172560.3 | P1 | ||
SSTR5 | ENST00000293897.7 | c.104C>T | p.Ser35Leu | missense_variant | 1/1 | P1 | |||
SSTR5 | ENST00000711615.1 | c.104C>T | p.Ser35Leu | missense_variant | 2/2 | P1 | |||
SSTR5 | ENST00000711616.1 | c.104C>T | p.Ser35Leu | missense_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000193 AC: 4AN: 207204Hom.: 0 AF XY: 0.0000176 AC XY: 2AN XY: 113796
GnomAD4 exome AF: 0.0000139 AC: 20AN: 1439374Hom.: 0 Cov.: 29 AF XY: 0.0000154 AC XY: 11AN XY: 714798
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.104C>T (p.S35L) 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 104, causing the serine (S) at amino acid position 35 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