chr6-41067119-T-C

Variant names:

• chr6-41067119-T-C
• rs11280
• NM_001329686.2:c.*216A>G

Variant summary

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

The NM_145063.4(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_145063.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145063.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OARD1	NM_001329686.2	MANE Select	c.*216A>G		3_prime_UTR	Exon 6 of 6	NP_001316615.1
	OARD1	NM_001329684.2		c.*216A>G		3_prime_UTR	Exon 8 of 8	NP_001316613.1
	OARD1	NM_001329685.1		c.*216A>G		3_prime_UTR	Exon 6 of 6	NP_001316614.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OARD1	ENST00000424266.7	TSL:2 MANE Select	c.*216A>G		3_prime_UTR	Exon 6 of 6	ENSP00000416829.2
	OARD1	ENST00000479950.5	TSL:1	c.*216A>G		3_prime_UTR	Exon 6 of 6	ENSP00000420484.1
	OARD1	ENST00000373154.6	TSL:1	c.*301A>G		3_prime_UTR	Exon 5 of 5	ENSP00000362247.2

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

African (AFR) AF: 0.446 AC: 2603 AN: 5838

American (AMR) AF: 0.340 AC: 2193 AN: 6456

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 1331 AN: 6740

East Asian (EAS) AF: 0.240 AC: 3989 AN: 16612

South Asian (SAS) AF: 0.264 AC: 2167 AN: 8218

European-Finnish (FIN) AF: 0.230 AC: 2902 AN: 12600

Middle Eastern (MID) AF: 0.241 AC: 243 AN: 1008

European-Non Finnish (NFE) AF: 0.220 AC: 24065 AN: 109172

Other (OTH) AF: 0.245 AC: 2737 AN: 11180

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

African (AFR) AF: 0.454 AC: 18832 AN: 41464

American (AMR) AF: 0.315 AC: 4820 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1326 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1395 AN: 4832

European-Finnish (FIN) AF: 0.229 AC: 2430 AN: 10590

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15760 AN: 67968

Other (OTH) AF: 0.270 AC: 569 AN: 2110

Alfa AF: 0.251 Hom.: 8717

Bravo AF: 0.314

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		-0.11
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11280; hg19: chr6-41034858;