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GeneBe

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

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
ADIPOQNM_004797.4 linkuse as main transcriptc.214+62G>C intron_variant ENST00000320741.7
ADIPOQ-AS1NR_046662.2 linkuse as main transcriptn.2216-92C>G intron_variant, non_coding_transcript_variant
ADIPOQNM_001177800.2 linkuse as main transcriptc.214+62G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADIPOQENST00000320741.7 linkuse as main transcriptc.214+62G>C intron_variant 1 NM_004797.4 P1
ADIPOQENST00000444204.2 linkuse as main transcriptc.214+62G>C intron_variant 1 P1
ADIPOQ-AS1ENST00000422718.1 linkuse as main transcriptn.2087-92C>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0000658
AC:
10
AN:
152074
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000849
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD4 exome
AF:
0.0000328
AC:
45
AN:
1373494
Hom.:
0
AF XY:
0.0000309
AC XY:
21
AN XY:
679084
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000832
Gnomad4 NFE exome
AF:
0.00000284
Gnomad4 OTH exome
AF:
0.0000175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
0.69
Dann
Benign
0.54

Splicing

Find out SpliceAI and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1501299; hg19: chr3-186571123;