rs12542166

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000254303 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254303	ENST00000523792.1	n.281+11018T>G		intron_variant	Intron 2 of 2	1
HAS2-AS1	ENST00000647560.1	n.447-22999A>C		intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000653591.1	n.764-22999A>C		intron_variant	Intron 6 of 6

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

Gnomad4 AFR AF: 0.0168

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.0589

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0785 Hom.: 140

Bravo AF: 0.0619

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12542166; hg19: chr8-122982838;