ENST00000647560.2:n.447-42622C>T

Variant names:

• chr8-121950976-C-T
• rs907121
• ENST00000647560.2:n.447-42622C>T

Variant summary

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

The ENST00000647560.2(HAS2-AS1):​n.447-42622C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,944 control chromosomes in the GnomAD database, including 13,281 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 0.41 (13281 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000647560.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 9 publications found

Genes affected

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

ENSG00000254303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647560.2. 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
	HAS2-AS1	ENST00000647560.2		n.447-42622C>T		intron	N/A
	HAS2-AS1	ENST00000653591.1		n.764-42622C>T		intron	N/A
	HAS2-AS1	ENST00000656261.1		n.753+37083C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61586 AN: 151826 Hom.: 13252 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.406 AC: 61671 AN: 151944 Hom.: 13281 Cov.: 32 AF XY: 0.409 AC XY: 30364 AN XY: 74230

African (AFR) AF: 0.547 AC: 22640 AN: 41420

American (AMR) AF: 0.410 AC: 6267 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3075 AN: 5168

South Asian (SAS) AF: 0.377 AC: 1813 AN: 4814

European-Finnish (FIN) AF: 0.346 AC: 3637 AN: 10522

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21755 AN: 67946

Other (OTH) AF: 0.387 AC: 817 AN: 2112

Alfa AF: 0.356 Hom.: 3107

Bravo AF: 0.416

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs907121; hg19: chr8-122963215;