rs2491252

Variant names:

• chr10-28524743-G-C
• rs2491252
• ENST00000527986.6:n.364-132C>G

Variant summary

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

The ENST00000527986.6(WAC-AS1):​n.364-132C>G variant causes a intron 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 ENST00000527986.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527986.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAC-AS1	NR_033805.1		n.682-132C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WAC-AS1	ENST00000527986.6	TSL:1	n.364-132C>G		intron	N/A
	WAC-AS1	ENST00000528337.2	TSL:1	n.723-132C>G		intron	N/A
	WAC-AS1	ENST00000664327.1		n.767-132C>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.400 AC: 4 AN: 10

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.655 AC: 27192 AN: 41500

American (AMR) AF: 0.599 AC: 9156 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3493 AN: 5166

South Asian (SAS) AF: 0.646 AC: 3110 AN: 4814

European-Finnish (FIN) AF: 0.427 AC: 4515 AN: 10566

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33825 AN: 67984

Other (OTH) AF: 0.561 AC: 1185 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2491252;

hg19: chr10-28813672;