chr2-11585767-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014668.4(GREB1):c.1021G>T(p.Ala341Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000955 in 1,612,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A341T) has been classified as Likely benign.
Frequency
Consequence
NM_014668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GREB1 | NM_014668.4 | c.1021G>T | p.Ala341Ser | missense_variant | 9/33 | ENST00000381486.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GREB1 | ENST00000381486.7 | c.1021G>T | p.Ala341Ser | missense_variant | 9/33 | 5 | NM_014668.4 | P1 | |
GREB1 | ENST00000234142.9 | c.1021G>T | p.Ala341Ser | missense_variant | 8/32 | 1 | P1 | ||
GREB1 | ENST00000381483.6 | c.1021G>T | p.Ala341Ser | missense_variant | 9/11 | 1 | |||
GREB1 | ENST00000263834.9 | c.1021G>T | p.Ala341Ser | missense_variant | 9/10 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000271 AC: 68AN: 251334Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135850
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1460614Hom.: 0 Cov.: 31 AF XY: 0.0000881 AC XY: 64AN XY: 726640
GnomAD4 genome AF: 0.000118 AC: 18AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.1021G>T (p.A341S) alteration is located in exon 9 (coding exon 8) of the GREB1 gene. This alteration results from a G to T substitution at nucleotide position 1021, causing the alanine (A) at amino acid position 341 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at