rs2491252

Positions:

• chr10-28524743-G-C

Variant summary

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

The NR_033805.1(WAC-AS1):​n.682-132C>G 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 0.559 in 152,114 control chromosomes in the GnomAD database, including 24,318 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 0.56 (24316 hom., cov: 33)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: WAC-AS1 NR_033805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

Genes affected

WAC-AS1 (HGNC:27347): (WAC antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WAC-AS1	NR_033805.1	n.682-132C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WAC-AS1	ENST00000527986.5	n.364-132C>G		intron_variant, non_coding_transcript_variant		1
WAC-AS1	ENST00000528337.2	n.723-132C>G		intron_variant, non_coding_transcript_variant		1
WAC-AS1	ENST00000664327.1	n.767-132C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84909 AN: 151980 Hom.: 24278 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.500 AC: 7 AN: 14 Hom.: 2 AF XY: 0.417 AC XY: 5 AN XY: 12

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.559 AC: 85003 AN: 152100 Hom.: 24316 Cov.: 33 AF XY: 0.562 AC XY: 41758 AN XY: 74362

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.561

Alfa AF: 0.532 Hom.: 2715

Bravo AF: 0.574

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2491252; hg19: chr10-28813672;