chr6-151808227-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000125.4(ESR1):c.315G>A(p.Pro105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 1,571,324 control chromosomes in the GnomAD database, including 13 homozygotes. 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. P105P) has been classified as Likely benign.
Frequency
Consequence
NM_000125.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESR1 | NM_000125.4 | c.315G>A | p.Pro105= | synonymous_variant | 1/8 | ENST00000206249.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESR1 | ENST00000206249.8 | c.315G>A | p.Pro105= | synonymous_variant | 1/8 | 1 | NM_000125.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00164 AC: 250AN: 152138Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.000820 AC: 143AN: 174452Hom.: 1 AF XY: 0.000610 AC XY: 58AN XY: 95096
GnomAD4 exome AF: 0.000166 AC: 235AN: 1419074Hom.: 2 Cov.: 36 AF XY: 0.000130 AC XY: 91AN XY: 701718
GnomAD4 genome ? AF: 0.00164 AC: 250AN: 152250Hom.: 11 Cov.: 32 AF XY: 0.00226 AC XY: 168AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
ESR1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 01, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at