chr7-137915917-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_194071.4(CREB3L2):c.415G>A(p.Val139Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,614,122 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 Uncertain significance (★).
Frequency
Consequence
NM_194071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CREB3L2 | NM_194071.4 | c.415G>A | p.Val139Ile | missense_variant | 3/12 | ENST00000330387.11 | |
CREB3L2 | NM_001318246.2 | c.226G>A | p.Val76Ile | missense_variant | 3/12 | ||
CREB3L2 | NM_001253775.2 | c.415G>A | p.Val139Ile | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CREB3L2 | ENST00000330387.11 | c.415G>A | p.Val139Ile | missense_variant | 3/12 | 1 | NM_194071.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251426Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135886
GnomAD4 exome AF: 0.000224 AC: 328AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.000235 AC XY: 171AN XY: 727222
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.415G>A (p.V139I) alteration is located in exon 3 (coding exon 3) of the CREB3L2 gene. This alteration results from a G to A substitution at nucleotide position 415, causing the valine (V) at amino acid position 139 to be replaced by an isoleucine (I). 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