17-46297604-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.2471C>T(p.Ala824Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/20 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: 3AN: 56846Hom.: 0 Cov.: 7 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000271 AC: 13AN: 479566Hom.: 0 Cov.: 4 AF XY: 0.0000156 AC XY: 4AN XY: 257012
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000528 AC: 3AN: 56846Hom.: 0 Cov.: 7 AF XY: 0.0000385 AC XY: 1AN XY: 25942
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2471C>T (p.A824V) 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 2471, causing the alanine (A) at amino acid position 824 to be replaced by a valine (V). 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