chr17-64858856-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_199340.5(LRRC37A3):c.4732T>C(p.Tyr1578His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,609,856 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4732T>C | p.Tyr1578His | missense_variant | 13/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+8869A>G | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.2086T>C | p.Tyr696His | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4732T>C | p.Tyr1578His | missense_variant | 13/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152088Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247730Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133692
GnomAD4 exome AF: 0.000172 AC: 251AN: 1457768Hom.: 0 Cov.: 31 AF XY: 0.000171 AC XY: 124AN XY: 725058
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152088Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.4732T>C (p.Y1578H) alteration is located in exon 12 (coding exon 10) of the LRRC37A3 gene. This alteration results from a T to C substitution at nucleotide position 4732, causing the tyrosine (Y) at amino acid position 1578 to be replaced by a histidine (H). 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