rs956225

Variant names:

• chr8-121897448-A-G
• rs956225
• ENST00000523550.1:n.315-5991A>G

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000523550.1(HAS2-AS1):​n.315-5991A>G variant causes a intron 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 ENST00000523550.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAS2-AS1	ENST00000523550.1	n.315-5991A>G		intron_variant	Intron 2 of 3	3
HAS2-AS1	ENST00000647560.1	n.446+17683A>G		intron_variant	Intron 3 of 3
HAS2-AS1	ENST00000648171.1	n.969-5991A>G		intron_variant	Intron 7 of 8

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;