5-173091051-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153607.3(CREBRF):c.872C>T(p.Pro291Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000369 in 1,614,048 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 (★).
Frequency
Consequence
NM_153607.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CREBRF | ENST00000296953.6 | c.872C>T | p.Pro291Leu | missense_variant | Exon 4 of 9 | 1 | NM_153607.3 | ENSP00000296953.2 | ||
CREBRF | ENST00000520420.5 | c.872C>T | p.Pro291Leu | missense_variant | Exon 4 of 4 | 1 | ENSP00000428290.1 | |||
CREBRF | ENST00000522692.5 | c.872C>T | p.Pro291Leu | missense_variant | Exon 4 of 4 | 1 | ENSP00000431107.1 | |||
CREBRF | ENST00000520464.1 | n.1149C>T | non_coding_transcript_exon_variant | Exon 4 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000287 AC: 72AN: 251120Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135726
GnomAD4 exome AF: 0.000394 AC: 576AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.000360 AC XY: 262AN XY: 727240
GnomAD4 genome AF: 0.000125 AC: 19AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.872C>T (p.P291L) alteration is located in exon 4 (coding exon 3) of the CREBRF gene. This alteration results from a C to T substitution at nucleotide position 872, causing the proline (P) at amino acid position 291 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