rs7846389

Variant names:

• chr8-121796367-C-A
• rs7846389
• ENST00000647560.1:n.311-83263C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-121796367-C-A
• chr8-121796367-C-G
• chr8-121796367-C-T

Variant summary

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

The ENST00000647560.1(HAS2-AS1):​n.311-83263C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,916 control chromosomes in the GnomAD database, including 23,396 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 0.54 (23396 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000647560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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.311-83263C>A		intron_variant	Intron 2 of 3
HAS2-AS1	ENST00000648171.1	n.885-66559C>A		intron_variant	Intron 6 of 8
HAS2-AS1	ENST00000653591.1	n.284-66559C>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82742 AN: 151798 Hom.: 23393 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.545 AC: 82774 AN: 151916 Hom.: 23396 Cov.: 32 AF XY: 0.548 AC XY: 40658 AN XY: 74216

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.543

Alfa AF: 0.582 Hom.: 10771

Bravo AF: 0.522

Asia WGS AF: 0.494 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.99
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7846389; hg19: chr8-122808607;