rs12783321

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047426123.1(LOC124902474):​c.305+261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,042 control chromosomes in the GnomAD database, including 27,817 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 0.60 ( 27817 hom., cov: 32)

Consequence

LOC124902474
XM_047426123.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539
Variant links:
Genes affected
ADIRF (HGNC:24043): (adipogenesis regulatory factor) APM2 gene is exclusively expressed in adipose tissue. Its function is currently unknown. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC124902474XM_047426123.1 linkuse as main transcriptc.305+261G>A intron_variant XP_047282079.1
AGAP11NR_171046.1 linkuse as main transcriptn.580+2603G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADIRFENST00000561504.1 linkuse as main transcriptc.*333+2603G>A intron_variant, NMD_transcript_variant 3 ENSP00000475582

Frequencies

GnomAD3 genomes
AF:
0.599
AC:
90968
AN:
151924
Hom.:
27788
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.514
Gnomad AMI
AF:
0.581
Gnomad AMR
AF:
0.656
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.921
Gnomad SAS
AF:
0.622
Gnomad FIN
AF:
0.693
Gnomad MID
AF:
0.557
Gnomad NFE
AF:
0.599
Gnomad OTH
AF:
0.611
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.599
AC:
91052
AN:
152042
Hom.:
27817
Cov.:
32
AF XY:
0.606
AC XY:
45042
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.514
Gnomad4 AMR
AF:
0.657
Gnomad4 ASJ
AF:
0.549
Gnomad4 EAS
AF:
0.920
Gnomad4 SAS
AF:
0.622
Gnomad4 FIN
AF:
0.693
Gnomad4 NFE
AF:
0.599
Gnomad4 OTH
AF:
0.614
Alfa
AF:
0.600
Hom.:
3449
Bravo
AF:
0.597
Asia WGS
AF:
0.721
AC:
2510
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.2
DANN
Benign
0.24

Splicing

Find out detailed SpliceAI scores 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: rs12783321; hg19: chr10-88733275; API