chr8-121970599-A-C

Variant names:

• chr8-121970599-A-C
• rs12542166
• ENST00000523792.1:n.281+11018T>G

Variant summary

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

The ENST00000523792.1(ENSG00000254303):​n.281+11018T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,242 control chromosomes in the GnomAD database, including 438 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 0.067 (438 hom., cov: 32)
• Consequence: ENSG00000254303 ENST00000523792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704
• Publications: 1 publications found

Genes affected

ENSG00000254303 (HGNC:):

HAS2-AS1 (HGNC:34340): (HAS2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523792.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254303	ENST00000523792.1	TSL:1	n.281+11018T>G		intron	N/A
	HAS2-AS1	ENST00000647560.2		n.447-22999A>C		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.764-22999A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10254 AN: 152124 Hom.: 435 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0622

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0675 AC: 10274 AN: 152242 Hom.: 438 Cov.: 32 AF XY: 0.0685 AC XY: 5097 AN XY: 74434

African (AFR) AF: 0.0168 AC: 698 AN: 41572

American (AMR) AF: 0.0841 AC: 1286 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.0589 AC: 305 AN: 5178

South Asian (SAS) AF: 0.102 AC: 493 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1208 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0862 AC: 5859 AN: 67998

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0636 Hom.: 215

Bravo AF: 0.0619

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.1
DANN	Benign	0.80
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs12542166; hg19: chr8-122982838;