rs759950184
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001114753.3(ENG):c.1845G>T(p.Ser615=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,598,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S615S) has been classified as Likely benign.
Frequency
Consequence
NM_001114753.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.1845G>T | p.Ser615= | synonymous_variant | 14/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.1845G>T | p.Ser615= | synonymous_variant | 14/14 | ||
ENG | NM_001278138.2 | c.1299G>T | p.Ser433= | synonymous_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.1845G>T | p.Ser615= | synonymous_variant | 14/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.1845G>T | p.Ser615= | synonymous_variant | 14/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.1299G>T | p.Ser433= | synonymous_variant | 14/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000762 AC: 17AN: 223130Hom.: 0 AF XY: 0.0000829 AC XY: 10AN XY: 120650
GnomAD4 exome AF: 0.00000830 AC: 12AN: 1446280Hom.: 0 Cov.: 31 AF XY: 0.00000696 AC XY: 5AN XY: 717998
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74344
ClinVar
Submissions by phenotype
ENG-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 19, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary hemorrhagic telangiectasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at