rs2072590
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000416928.8(HAGLR):n.234T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 169,404 control chromosomes in the GnomAD database, including 48,939 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 0.76 ( 44767 hom., cov: 32)
Exomes 𝑓: 0.69 ( 4172 hom. )
Consequence
HAGLR
ENST00000416928.8 non_coding_transcript_exon
ENST00000416928.8 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.130
Genes affected
HAGLR (HGNC:43755): (HOXD antisense growth-associated long non-coding RNA)
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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=-0.72).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAGLR | NR_033979.2 | n.146-411T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAGLROS | ENST00000426615.4 | n.189A>C | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
HAGLR | ENST00000452365.2 | n.184-49T>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.761 AC: 115710AN: 151998Hom.: 44711 Cov.: 32
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GnomAD4 exome AF: 0.694 AC: 11990AN: 17288Hom.: 4172 Cov.: 0 AF XY: 0.691 AC XY: 6316AN XY: 9134
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GnomAD4 genome ? AF: 0.761 AC: 115820AN: 152116Hom.: 44767 Cov.: 32 AF XY: 0.764 AC XY: 56820AN XY: 74332
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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