chr2-11585168-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_014668.4(GREB1):c.909G>A(p.Leu303=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,562,232 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 4 hom. )
Consequence
GREB1
NM_014668.4 synonymous
NM_014668.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.942
Genes affected
GREB1 (HGNC:24885): (growth regulating estrogen receptor binding 1) This gene is an estrogen-responsive gene that is an early response gene in the estrogen receptor-regulated pathway. It is thought to play an important role in hormone-responsive tissues and cancer. Three alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 2-11585168-G-A is Benign according to our data. Variant chr2-11585168-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650680.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.942 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GREB1 | NM_014668.4 | c.909G>A | p.Leu303= | synonymous_variant | 8/33 | ENST00000381486.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GREB1 | ENST00000381486.7 | c.909G>A | p.Leu303= | synonymous_variant | 8/33 | 5 | NM_014668.4 | P1 | |
GREB1 | ENST00000234142.9 | c.909G>A | p.Leu303= | synonymous_variant | 7/32 | 1 | P1 | ||
GREB1 | ENST00000381483.6 | c.909G>A | p.Leu303= | synonymous_variant | 8/11 | 1 | |||
GREB1 | ENST00000263834.9 | c.909G>A | p.Leu303= | synonymous_variant | 8/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00125 AC: 190AN: 152126Hom.: 0 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
190
AN:
152126
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00110 AC: 233AN: 212508Hom.: 0 AF XY: 0.000936 AC XY: 108AN XY: 115404
GnomAD3 exomes
AF:
AC:
233
AN:
212508
Hom.:
AF XY:
AC XY:
108
AN XY:
115404
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00171 AC: 2416AN: 1409990Hom.: 4 Cov.: 30 AF XY: 0.00160 AC XY: 1120AN XY: 698632
GnomAD4 exome
AF:
AC:
2416
AN:
1409990
Hom.:
Cov.:
30
AF XY:
AC XY:
1120
AN XY:
698632
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00125 AC: 190AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.00106 AC XY: 79AN XY: 74444
GnomAD4 genome
?
AF:
AC:
190
AN:
152242
Hom.:
Cov.:
33
AF XY:
AC XY:
79
AN XY:
74444
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | GREB1: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at