12-75343862-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001304964.2(GLIPR1L1):c.344C>T(p.Thr115Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000819 in 1,611,536 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_001304964.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151988Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251172Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135778
GnomAD4 exome AF: 0.0000829 AC: 121AN: 1459430Hom.: 0 Cov.: 29 AF XY: 0.0000744 AC XY: 54AN XY: 726186
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152106Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.344C>T (p.T115M) alteration is located in exon 2 (coding exon 2) of the GLIPR1L1 gene. This alteration results from a C to T substitution at nucleotide position 344, causing the threonine (T) at amino acid position 115 to be replaced by a methionine (M). 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