rs12783321

chr10-86973518-G-Achr10-86973518-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LOC124902474 (HGNC:):

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

ACMG classification

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	UniProt
LOC124902474	XM_047426123.1	c.305+261G>A		intron_variant
AGAP11	NR_171046.1	n.580+2603G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIRF	ENST00000561504.1	c.*333+2603G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90968 AN: 151924 Hom.: 27788 Cov.: 32

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

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

Other links and lift over

dbSNP: rs12783321; hg19: chr10-88733275;