rs1501299
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong
The NM_004797(ADIPOQ):c.214+62G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000658 in 152074 control chromosomes in the gnomAD Genomes database, including 1 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 0.000066 ( 1 hom., cov: 33)
Consequence
ADIPOQ
NM_004797 intron
NM_004797 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.683
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.0000658 (10/152074) . There are 1 homozygotes in gnomad. There are 8 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADIPOQ | NM_004797.4 | c.214+62G>C | intron_variant | ENST00000320741.7 | |||
ADIPOQ-AS1 | NR_046662.2 | n.2216-92C>G | intron_variant, non_coding_transcript_variant | ||||
ADIPOQ | NM_001177800.2 | c.214+62G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADIPOQ | ENST00000320741.7 | c.214+62G>C | intron_variant | 1 | NM_004797.4 | P1 | |||
ADIPOQ | ENST00000444204.2 | c.214+62G>C | intron_variant | 1 | P1 | ||||
ADIPOQ-AS1 | ENST00000422718.1 | n.2087-92C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152074Hom.: 1 Cov.: 33
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GnomAD4 exome AF: 0.0000328 AC: 45AN: 1373494Hom.: 0 AF XY: 0.0000309 AC XY: 21AN XY: 679084
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at