chr7-137928200-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_194071.4(CREB3L2):c.269G>A(p.Arg90Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000231 in 1,602,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R90W) has been classified as Uncertain significance.
Frequency
Consequence
NM_194071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREB3L2 | NM_194071.4 | c.269G>A | p.Arg90Gln | missense_variant | 2/12 | ENST00000330387.11 | |
CREB3L2 | NM_001318246.2 | c.80G>A | p.Arg27Gln | missense_variant | 2/12 | ||
CREB3L2 | NM_001253775.2 | c.269G>A | p.Arg90Gln | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREB3L2 | ENST00000330387.11 | c.269G>A | p.Arg90Gln | missense_variant | 2/12 | 1 | NM_194071.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 3AN: 230430Hom.: 0 AF XY: 0.00000803 AC XY: 1AN XY: 124600
GnomAD4 exome AF: 0.0000235 AC: 34AN: 1449894Hom.: 0 Cov.: 34 AF XY: 0.0000222 AC XY: 16AN XY: 720242
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2022 | The c.269G>A (p.R90Q) alteration is located in exon 2 (coding exon 2) of the CREB3L2 gene. This alteration results from a G to A substitution at nucleotide position 269, causing the arginine (R) at amino acid position 90 to be replaced by a glutamine (Q). 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