rs956225

Positions:

• chr8-121897448-A-G
• chr8-121897448-A-T

Variant summary

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

The ENST00000664717.1(HAS2-AS1):​n.959+8471A>G 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 0.119 in 152,150 control chromosomes in the GnomAD database, including 1,325 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 0.12 (1325 hom., cov: 32)
• Consequence: HAS2-AS1 ENST00000664717.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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	ENST00000664717.1	n.959+8471A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18108 AN: 152032 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.119 AC: 18104 AN: 152150 Hom.: 1325 Cov.: 32 AF XY: 0.122 AC XY: 9107 AN XY: 74382

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.132

Alfa AF: 0.146 Hom.: 3642

Bravo AF: 0.109

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs956225; hg19: chr8-122909687;