rs2293004

Positions:

• chr3-151814106-C-T

Variant summary

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

The NR_110203.1(AADACL2-AS1):​n.320-39441G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,589,212 control chromosomes in the GnomAD database, including 80,337 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 0.31 (7490 hom., cov: 31)
  • Exomes 𝑓: 0.31 (72847 hom.)
• Consequence: AADACL2-AS1 NR_110203.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

Genes affected

AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

AADAC (HGNC:17): (arylacetamide deacetylase) Microsomal arylacetamide deacetylase competes against the activity of cytosolic arylamine N-acetyltransferase, which catalyzes one of the initial biotransformation pathways for arylamine and heterocyclic amine carcinogens [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AADACL2-AS1	NR_110203.1	n.320-39441G>A		intron_variant, non_coding_transcript_variant
AADACL2-AS1	NR_110202.1	n.320-39441G>A		intron_variant, non_coding_transcript_variant
AADAC	NM_001086.3			upstream_gene_variant		ENST00000232892.12	NP_001077.2
AADAC	XM_005247104.5			upstream_gene_variant			XP_005247161.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AADACL2-AS1	ENST00000483843.6	n.440-39441G>A		intron_variant, non_coding_transcript_variant		5
AADAC	ENST00000488869.1	c.-57C>T		5_prime_UTR_variant	1/4	2		ENSP00000419620
AADACL2-AS1	ENST00000475855.1	n.320-39441G>A		intron_variant, non_coding_transcript_variant		5
AADAC	ENST00000232892.12			upstream_gene_variant		1	NM_001086.3	ENSP00000232892	P1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46281 AN: 151540 Hom.: 7482 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.310

GnomAD4 exome AF: 0.312 AC: 447979 AN: 1437554 Hom.: 72847 Cov.: 27 AF XY: 0.310 AC XY: 222439 AN XY: 716612

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.280

Gnomad4 EAS exome AF: 0.315

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.218

Gnomad4 NFE exome AF: 0.319

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.305 AC: 46314 AN: 151658 Hom.: 7490 Cov.: 31 AF XY: 0.299 AC XY: 22154 AN XY: 74062

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.310

Alfa AF: 0.318 Hom.: 15696

Bravo AF: 0.316

Asia WGS AF: 0.284 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs2293004; hg19: chr3-151531894; COSMIC: COSV51761050;