1-74041892-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001105659.2(LRRIQ3):c.1039A>G(p.Thr347Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000585 in 1,606,686 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 Likely benign (★).
Frequency
Consequence
NM_001105659.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRIQ3 | NM_001105659.2 | c.1039A>G | p.Thr347Ala | missense_variant | 7/8 | ENST00000354431.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRIQ3 | ENST00000354431.9 | c.1039A>G | p.Thr347Ala | missense_variant | 7/8 | 5 | NM_001105659.2 | P2 | |
LRRIQ3 | ENST00000395089.5 | c.1039A>G | p.Thr347Ala | missense_variant | 6/7 | 5 | P2 | ||
LRRIQ3 | ENST00000417067.5 | c.131-14923A>G | intron_variant | 2 | |||||
LRRIQ3 | ENST00000415760.5 | c.*2502A>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 244126Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132686
GnomAD4 exome AF: 0.0000612 AC: 89AN: 1454604Hom.: 0 Cov.: 31 AF XY: 0.0000609 AC XY: 44AN XY: 722776
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at