rs7846389

Positions:

• 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 ENST00000664717.1(HAS2-AS1):​n.671-83263C>A variant causes a intron, non coding transcript 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 ENST00000664717.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAS2-AS1	ENST00000664717.1	n.671-83263C>A		intron_variant, non_coding_transcript_variant

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;