chr16-1078894-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001172560.3(SSTR5):c.26C>T(p.Thr9Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000929 in 1,606,448 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T9A) 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSTR5 | NM_001172560.3 | c.26C>T | p.Thr9Met | missense_variant | 2/2 | ENST00000689027.1 | |
SSTR5 | NM_001053.4 | c.26C>T | p.Thr9Met | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSTR5 | ENST00000689027.1 | c.26C>T | p.Thr9Met | missense_variant | 2/2 | NM_001172560.3 | P1 | ||
SSTR5 | ENST00000293897.7 | c.26C>T | p.Thr9Met | missense_variant | 1/1 | P1 | |||
SSTR5 | ENST00000711615.1 | c.26C>T | p.Thr9Met | missense_variant | 2/2 | P1 | |||
SSTR5 | ENST00000711616.1 | c.26C>T | p.Thr9Met | missense_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.00228 AC: 347AN: 152194Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00136 AC: 318AN: 234020Hom.: 1 AF XY: 0.00119 AC XY: 154AN XY: 129006
GnomAD4 exome AF: 0.000787 AC: 1144AN: 1454138Hom.: 4 Cov.: 29 AF XY: 0.000732 AC XY: 530AN XY: 723562
GnomAD4 genome ? AF: 0.00228 AC: 348AN: 152310Hom.: 4 Cov.: 33 AF XY: 0.00240 AC XY: 179AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at