chr10-86973518-G-A

Variant names:

• chr10-86973518-G-A
• rs12783321
• ENST00000725870.1:n.298C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725870.1(ADIRF-AS1):​n.298C>T variant causes a non coding transcript exon 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: ADIRF-AS1 ENST00000725870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 5 publications found

Genes affected

ADIRF-AS1 (HGNC:45127): (ADIRF antisense RNA 1)

ENSG00000151303 (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]

AGAP11 (HGNC:29421): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 11) Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AGAP11	NR_171046.1	n.580+2603G>A		intron_variant	Intron 1 of 10
LOC124902474	XM_047426123.1	c.305+261G>A		intron_variant	Intron 2 of 2		XP_047282079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIRF-AS1	ENST00000725870.1	n.298C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000151303	ENST00000433214.2	n.175+2603G>A		intron_variant	Intron 1 of 11	2
ADIRF	ENST00000561504.2	n.*333+2603G>A		intron_variant	Intron 3 of 4	3		ENSP00000475582.1

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

African (AFR) AF: 0.514 AC: 21322 AN: 41450

American (AMR) AF: 0.657 AC: 10033 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1907 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4766 AN: 5178

South Asian (SAS) AF: 0.622 AC: 2987 AN: 4806

European-Finnish (FIN) AF: 0.693 AC: 7313 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40731 AN: 67982

Other (OTH) AF: 0.614 AC: 1296 AN: 2112

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs12783321; hg19: chr10-88733275;