chr17-46540856-A-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_001006607.3(LRRC37A2):c.3028A>C(p.Met1010Leu) 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M1010V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001006607.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A2 | NM_001006607.3 | c.3028A>C | p.Met1010Leu | missense_variant | 7/14 | ENST00000576629.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A2 | ENST00000576629.6 | c.3028A>C | p.Met1010Leu | missense_variant | 7/14 | 5 | NM_001006607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 5AN: 141720Hom.: 0 Cov.: 23 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000552 AC: 672AN: 1217016Hom.: 0 Cov.: 21 AF XY: 0.000487 AC XY: 299AN XY: 613656
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000353 AC: 5AN: 141720Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 2AN XY: 68764
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.3028A>C (p.M1010L) alteration is located in exon 7 (coding exon 7) of the LRRC37A2 gene. This alteration results from a A to C substitution at nucleotide position 3028, causing the methionine (M) at amino acid position 1010 to be replaced by a leucine (L). 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