rs11280

Positions:

• chr6-41067119-T-C
• chr6-41067119-T-G

Variant summary

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

The NM_001329686.2(OARD1):​c.*216A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 329,912 control chromosomes in the GnomAD database, including 13,186 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 0.30 (7831 hom., cov: 32)
  • Exomes 𝑓: 0.24 (5355 hom.)
• Consequence: OARD1 NM_001329686.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

OARD1 (HGNC:21257): (O-acyl-ADP-ribose deacylase 1) The protein encoded by this gene is a deacylase that can convert O-acetyl-ADP-ribose to ADP-ribose and acetate, O-propionyl-ADP-ribose to ADP-ribose and propionate, and O-butyryl-ADP-ribose to ADP-ribose and butyrate. The ADP-ribose product is able to inhibit these reactions through a competitive feedback loop. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OARD1	NM_001329686.2	c.*216A>G		3_prime_UTR_variant	6/6	ENST00000424266.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OARD1	ENST00000424266.7	c.*216A>G		3_prime_UTR_variant	6/6	2	NM_001329686.2	P1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46024 AN: 151970 Hom.: 7821 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.237 AC: 42230 AN: 177824 Hom.: 5355 Cov.: 2 AF XY: 0.235 AC XY: 21772 AN XY: 92538

Gnomad4 AFR exome AF: 0.446

Gnomad4 AMR exome AF: 0.340

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.240

Gnomad4 SAS exome AF: 0.264

Gnomad4 FIN exome AF: 0.230

Gnomad4 NFE exome AF: 0.220

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.303 AC: 46073 AN: 152088 Hom.: 7831 Cov.: 32 AF XY: 0.301 AC XY: 22355 AN XY: 74338

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.270

Alfa AF: 0.243 Hom.: 6404

Bravo AF: 0.314

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11280; hg19: chr6-41034858;