chr17-64859494-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_199340.5(LRRC37A3):c.4652A>T(p.Tyr1551Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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.4652A>T | p.Tyr1551Phe | missense_variant | 12/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+9507T>A | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.2006A>T | p.Tyr669Phe | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4652A>T | p.Tyr1551Phe | missense_variant | 12/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.4652A>T (p.Y1551F) alteration is located in exon 11 (coding exon 9) of the LRRC37A3 gene. This alteration results from a A to T substitution at nucleotide position 4652, causing the tyrosine (Y) at amino acid position 1551 to be replaced by a phenylalanine (F). 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
Publications
No publications associated with this variant yet.