3-169822345-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001080460.3(LRRIQ4):c.424C>T(p.His142Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,682 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080460.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRIQ4 | ENST00000340806.7 | c.424C>T | p.His142Tyr | missense_variant | Exon 2 of 6 | 5 | NM_001080460.3 | ENSP00000342188.6 | ||
LRRIQ4 | ENST00000691416.1 | c.424C>T | p.His142Tyr | missense_variant | Exon 2 of 5 | ENSP00000508855.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248702Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135004
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461458Hom.: 3 Cov.: 33 AF XY: 0.0000715 AC XY: 52AN XY: 727004
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.424C>T (p.H142Y) alteration is located in exon 1 (coding exon 1) of the LRRIQ4 gene. This alteration results from a C to T substitution at nucleotide position 424, causing the histidine (H) at amino acid position 142 to be replaced by a tyrosine (Y). 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