chr12-75391348-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001270396.2(GLIPR1L2):c.232A>T(p.Met78Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,382 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001270396.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLIPR1L2 | NM_001270396.2 | c.232A>T | p.Met78Leu | missense_variant, splice_region_variant | 1/6 | ENST00000550916.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLIPR1L2 | ENST00000550916.6 | c.232A>T | p.Met78Leu | missense_variant, splice_region_variant | 1/6 | 1 | NM_001270396.2 | P1 | |
GLIPR1L2 | ENST00000320460.8 | c.232A>T | p.Met78Leu | missense_variant, splice_region_variant | 1/4 | 1 | |||
GLIPR1L2 | ENST00000378692.7 | c.-220A>T | splice_region_variant, 5_prime_UTR_variant | 1/7 | 1 | ||||
GLIPR1L2 | ENST00000547164.1 | c.232A>T | p.Met78Leu | missense_variant, splice_region_variant | 1/3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461382Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727068
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.232A>T (p.M78L) alteration is located in exon 1 (coding exon 1) of the GLIPR1L2 gene. This alteration results from a A to T substitution at nucleotide position 232, causing the methionine (M) at amino acid position 78 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