17-46297456-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.2323C>T(p.Pro775Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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: 5AN: 125342Hom.: 0 Cov.: 18 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000868 AC: 11AN: 1266728Hom.: 1 Cov.: 29 AF XY: 0.00000628 AC XY: 4AN XY: 636558
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000399 AC: 5AN: 125342Hom.: 0 Cov.: 18 AF XY: 0.0000502 AC XY: 3AN XY: 59710
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2323C>T (p.P775S) 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 2323, causing the proline (P) at amino acid position 775 to be replaced by a serine (S). 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