chr17-16491839-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001113567.3(LRRC75A):āc.152A>Gā(p.Tyr51Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000799 in 1,252,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001113567.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC75A | NM_001113567.3 | c.152A>G | p.Tyr51Cys | missense_variant | 1/4 | ENST00000470794.2 | |
LOC124903936 | XR_007065641.1 | n.1605+4393T>C | intron_variant, non_coding_transcript_variant | ||||
LRRC75A | NM_207387.4 | c.152A>G | p.Tyr51Cys | missense_variant | 1/3 | ||
LRRC75A | XM_047435962.1 | c.152A>G | p.Tyr51Cys | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC75A | ENST00000470794.2 | c.152A>G | p.Tyr51Cys | missense_variant | 1/4 | 1 | NM_001113567.3 | P1 | |
LRRC75A | ENST00000409083.7 | c.152A>G | p.Tyr51Cys | missense_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.99e-7 AC: 1AN: 1252138Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 616892
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.152A>G (p.Y51C) alteration is located in exon 1 (coding exon 1) of the LRRC75A gene. This alteration results from a A to G substitution at nucleotide position 152, causing the tyrosine (Y) at amino acid position 51 to be replaced by a cysteine (C). 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.