chr6-151807928-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000125.4(ESR1):c.16C>T(p.His6Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0045 in 1,613,882 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000125.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00309 AC: 470AN: 152198Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00327 AC: 811AN: 248082Hom.: 2 AF XY: 0.00323 AC XY: 435AN XY: 134520
GnomAD4 exome AF: 0.00465 AC: 6791AN: 1461566Hom.: 23 Cov.: 30 AF XY: 0.00449 AC XY: 3266AN XY: 727092
GnomAD4 genome AF: 0.00308 AC: 469AN: 152316Hom.: 1 Cov.: 32 AF XY: 0.00273 AC XY: 203AN XY: 74468
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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Identified in an individual with primary ovarian insufficiency, however, functional studies in HEK293T cells demonstrated that the variant showed similar transcriptional activity to wild type (PMID: 27603904); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23074960, 27603904, 34662886, 36099812) -
ESR1: PP3, BS2 -
ESR1-related disorder Benign:1
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