8-144522552-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001024678.4(LRRC24):c.1465G>A(p.Ala489Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000724 in 1,533,674 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_001024678.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC24 | ENST00000529415.7 | c.1465G>A | p.Ala489Thr | missense_variant | Exon 5 of 5 | 1 | NM_001024678.4 | ENSP00000434849.1 | ||
LRRC14 | ENST00000292524.6 | c.*1074C>T | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_014665.4 | ENSP00000292524.1 | |||
LRRC24 | ENST00000533758.1 | c.1456G>A | p.Ala486Thr | missense_variant | Exon 5 of 5 | 5 | ENSP00000435653.1 | |||
LRRC14 | ENST00000528528.1 | n.-30C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000723 AC: 10AN: 138218Hom.: 0 AF XY: 0.000117 AC XY: 9AN XY: 77208
GnomAD4 exome AF: 0.0000775 AC: 107AN: 1381488Hom.: 0 Cov.: 32 AF XY: 0.0000762 AC XY: 52AN XY: 682800
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1465G>A (p.A489T) alteration is located in exon 5 (coding exon 4) of the LRRC24 gene. This alteration results from a G to A substitution at nucleotide position 1465, causing the alanine (A) at amino acid position 489 to be replaced by a threonine (T). 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