1-74041915-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001105659.2(LRRIQ3):c.1016A>C(p.Glu339Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00018 in 1,604,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001105659.2 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 |
---|---|---|---|---|---|---|---|
LRRIQ3 | NM_001105659.2 | c.1016A>C | p.Glu339Ala | missense_variant | 7/8 | ENST00000354431.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRIQ3 | ENST00000354431.9 | c.1016A>C | p.Glu339Ala | missense_variant | 7/8 | 5 | NM_001105659.2 | P2 | |
LRRIQ3 | ENST00000395089.5 | c.1016A>C | p.Glu339Ala | missense_variant | 6/7 | 5 | P2 | ||
LRRIQ3 | ENST00000417067.5 | c.131-14946A>C | intron_variant | 2 | |||||
LRRIQ3 | ENST00000415760.5 | c.*2479A>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000949 AC: 23AN: 242306Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 131970
GnomAD4 exome AF: 0.000193 AC: 280AN: 1452180Hom.: 0 Cov.: 31 AF XY: 0.000184 AC XY: 133AN XY: 721538
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.1016A>C (p.E339A) alteration is located in exon 7 (coding exon 6) of the LRRIQ3 gene. This alteration results from a A to C substitution at nucleotide position 1016, causing the glutamic acid (E) at amino acid position 339 to be replaced by an alanine (A). 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