rs10106208

Positions:

• chr8-121733090-G-A

Variant summary

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

The ENST00000664717.1(HAS2-AS1):​n.670+25415G>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 0.0657 in 152,192 control chromosomes in the GnomAD database, including 431 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 0.066 (431 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000664717.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0955 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.670+25415G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10006 AN: 152074 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0657 AC: 10005 AN: 152192 Hom.: 431 Cov.: 32 AF XY: 0.0639 AC XY: 4754 AN XY: 74414

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.0888

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.0646

Alfa AF: 0.0873 Hom.: 324

Bravo AF: 0.0604

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10106208; hg19: chr8-122745330;