8-121950976-C-T

Variant names:

• chr8-121950976-C-T
• rs907121
• ENST00000647560.1:n.447-42622C>T

Variant summary

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

The ENST00000647560.1(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 ENST00000647560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

Genes affected

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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
HAS2-AS1	ENST00000647560.1	n.447-42622C>T		intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000653591.1	n.764-42622C>T		intron_variant	Intron 6 of 6
HAS2-AS1	ENST00000656261.1	n.753+37083C>T		intron_variant	Intron 6 of 6

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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.387

Alfa AF: 0.290 Hom.: 1044

Bravo AF: 0.416

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907121; hg19: chr8-122963215;