17-46297514-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_014834.4(LRRC37A):c.2381C>T(p.Pro794Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 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. P794S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014834.4 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: 0.00 AC: 7AN: 63232Hom.: 0 Cov.: 8 FAILED QC
GnomAD3 exomes AF: 0.000133 AC: 4AN: 30028Hom.: 0 AF XY: 0.0000661 AC XY: 1AN XY: 15138
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000200 AC: 12AN: 600908Hom.: 0 Cov.: 7 AF XY: 0.0000123 AC XY: 4AN XY: 323990
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000111 AC: 7AN: 63300Hom.: 0 Cov.: 8 AF XY: 0.000136 AC XY: 4AN XY: 29392
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2381C>T (p.P794L) alteration is located in exon 1 (coding exon 1) of the LRRC37A gene. This alteration results from a C to T substitution at nucleotide position 2381, causing the proline (P) at amino acid position 794 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