rs10089677

Positions:

• chr8-121648008-G-A
• chr8-121648008-G-C

Variant summary

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

The ENST00000648171.1(HAS2-AS1):​n.752+3617G>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 0.611 in 152,020 control chromosomes in the GnomAD database, including 29,929 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 0.61 (29929 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000648171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAS2-AS1	ENST00000648171.1	n.752+3617G>A		intron_variant, non_coding_transcript_variant
HAS2-AS1	ENST00000663147.1	n.728+3617G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92722 AN: 151902 Hom.: 29881 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.611 AC: 92827 AN: 152020 Hom.: 29929 Cov.: 32 AF XY: 0.611 AC XY: 45431 AN XY: 74300

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.613

Alfa AF: 0.530 Hom.: 29312

Bravo AF: 0.631

Asia WGS AF: 0.723 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10089677; hg19: chr8-122660248;