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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.683

Links

ADIPOQ (HGNC:13633):

ADIPOQ-AS1 (HGNC:40648):

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	Effect	MANE
ADIPOQ	NM_004797.4 linkuse as main transcript	c.214+62G>C	intron_variant	ENST00000320741.7
ADIPOQ-AS1	NR_046662.2 linkuse as main transcript	n.2216-92C>G	intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2 linkuse as main transcript	c.214+62G>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
ADIPOQ	ENST00000320741.7 linkuse as main transcript	c.214+62G>C	intron_variant	1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2 linkuse as main transcript	c.214+62G>C	intron_variant	1		P1
ADIPOQ-AS1	ENST00000422718.1 linkuse as main transcript	n.2087-92C>G	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0000658

AC:

AN:

152074

Hom.:

Cov.:

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:

AN:

1373494

Hom.:

AF XY:

0.0000309

AC XY:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over