17-64859787-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_199340.5(LRRC37A3):āc.4359C>Gā(p.Asp1453Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,210 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_199340.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4359C>G | p.Asp1453Glu | missense_variant | 12/15 | ENST00000584306.6 | NP_955372.2 | |
LOC105376844 | XR_934912.4 | n.177+9800G>C | intron_variant, non_coding_transcript_variant | |||||
LRRC37A3 | NM_001303255.3 | c.1713C>G | p.Asp571Glu | missense_variant | 8/11 | NP_001290184.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4359C>G | p.Asp1453Glu | missense_variant | 12/15 | 1 | NM_199340.5 | ENSP00000464535 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151922Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250502Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135678
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460288Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726440
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151922Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 5AN XY: 74156
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 15, 2023 | The c.4359C>G (p.D1453E) alteration is located in exon 11 (coding exon 9) of the LRRC37A3 gene. This alteration results from a C to G substitution at nucleotide position 4359, causing the aspartic acid (D) at amino acid position 1453 to be replaced by a glutamic acid (E). 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