chr2-11585767-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014668.4(GREB1):c.1021G>A(p.Ala341Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,612,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. A341S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GREB1 | NM_014668.4 | c.1021G>A | p.Ala341Thr | missense_variant | 9/33 | ENST00000381486.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GREB1 | ENST00000381486.7 | c.1021G>A | p.Ala341Thr | missense_variant | 9/33 | 5 | NM_014668.4 | P1 | |
GREB1 | ENST00000234142.9 | c.1021G>A | p.Ala341Thr | missense_variant | 8/32 | 1 | P1 | ||
GREB1 | ENST00000381483.6 | c.1021G>A | p.Ala341Thr | missense_variant | 9/11 | 1 | |||
GREB1 | ENST00000263834.9 | c.1021G>A | p.Ala341Thr | missense_variant | 9/10 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251334Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135850
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460614Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726640
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | 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