1-161756789-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007240.3(DUSP12):c.865C>T(p.Leu289Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000823 in 1,457,972 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. L289I) has been classified as Uncertain significance.
Frequency
Consequence
NM_007240.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DUSP12 | NM_007240.3 | c.865C>T | p.Leu289Phe | missense_variant | 6/6 | ENST00000367943.5 | |
DUSP12 | XM_005244862.4 | c.475C>T | p.Leu159Phe | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DUSP12 | ENST00000367943.5 | c.865C>T | p.Leu289Phe | missense_variant | 6/6 | 1 | NM_007240.3 | P1 | |
ATF6-DT | ENST00000702792.1 | n.373-6422G>A | intron_variant, non_coding_transcript_variant | ||||||
DUSP12 | ENST00000484291.5 | c.*345C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457972Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 4AN XY: 725206
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.865C>T (p.L289F) alteration is located in exon 6 (coding exon 6) of the DUSP12 gene. This alteration results from a C to T substitution at nucleotide position 865, causing the leucine (L) at amino acid position 289 to be replaced by a phenylalanine (F). 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