chr17-64855876-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_199340.5(LRRC37A3):c.4823G>A(p.Arg1608Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,611,764 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_199340.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4823G>A | p.Arg1608Gln | missense_variant | 14/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+5889C>T | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.2177G>A | p.Arg726Gln | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4823G>A | p.Arg1608Gln | missense_variant | 14/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251068Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135690
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459478Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726050
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152286Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.4823G>A (p.R1608Q) alteration is located in exon 13 (coding exon 11) of the LRRC37A3 gene. This alteration results from a G to A substitution at nucleotide position 4823, causing the arginine (R) at amino acid position 1608 to be replaced by a glutamine (Q). 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