rs7288847
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The XM_047441696.1(LOC124905135):c.*8714C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000821 in 182,782 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000092 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
LOC124905135
XM_047441696.1 3_prime_UTR
XM_047441696.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0720
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124905135 | XM_047441696.1 | c.*8714C>A | 3_prime_UTR_variant | 2/2 | |||
MIRLET7BHG | NR_027033.2 | n.4092C>A | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIRLET7BHG | ENST00000360737.4 | n.3935C>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152084Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.0000326 AC: 1AN: 30698Hom.: 0 Cov.: 0 AF XY: 0.0000610 AC XY: 1AN XY: 16386
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GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152084Hom.: 0 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74272
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at