7-137882493-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_194071.4(CREB3L2):c.1406C>T(p.Pro469Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREB3L2 | NM_194071.4 | c.1406C>T | p.Pro469Leu | missense_variant | 11/12 | ENST00000330387.11 | |
CREB3L2 | NM_001318246.2 | c.1217C>T | p.Pro406Leu | missense_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREB3L2 | ENST00000330387.11 | c.1406C>T | p.Pro469Leu | missense_variant | 11/12 | 1 | NM_194071.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251386Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135872
GnomAD4 exome AF: 0.0000581 AC: 85AN: 1461762Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727194
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.1406C>T (p.P469L) alteration is located in exon 11 (coding exon 11) of the CREB3L2 gene. This alteration results from a C to T substitution at nucleotide position 1406, causing the proline (P) at amino acid position 469 to be replaced by a leucine (L). 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