rs3751972
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001076680.3(LYRM9):c.*85G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 1,443,304 control chromosomes in the GnomAD database, including 407,561 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.80 ( 49485 hom., cov: 34)
Exomes 𝑓: 0.74 ( 358076 hom. )
Consequence
LYRM9
NM_001076680.3 3_prime_UTR
NM_001076680.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.01
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYRM9 | NM_001076680.3 | c.*85G>T | 3_prime_UTR_variant | 4/4 | ENST00000379102.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYRM9 | ENST00000379102.8 | c.*85G>T | 3_prime_UTR_variant | 4/4 | 2 | NM_001076680.3 | P1 | ||
ENST00000581901.1 | n.417C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.799 AC: 121608AN: 152142Hom.: 49413 Cov.: 34
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GnomAD4 exome AF: 0.743 AC: 958725AN: 1291044Hom.: 358076 Cov.: 18 AF XY: 0.743 AC XY: 474409AN XY: 638290
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GnomAD4 genome ? AF: 0.800 AC: 121742AN: 152260Hom.: 49485 Cov.: 34 AF XY: 0.802 AC XY: 59700AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at