rs9322079

Variant names:

• chr6-146861203-A-G
• rs9322079
• ENST00000427394.5:n.551-460T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427394.5(STXBP5-AS1):​n.551-460T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,986 control chromosomes in the GnomAD database, including 22,086 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 (22086 hom., cov: 32)
• Consequence: STXBP5-AS1 ENST00000427394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 3 publications found

Genes affected

STXBP5-AS1 (HGNC:44183): (STXBP5 antisense RNA 1)

ENSG00000227748 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP5-AS1	NR_034115.1	n.625-460T>C		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP5-AS1	ENST00000427394.5	n.551-460T>C		intron_variant	Intron 7 of 10	1
STXBP5-AS1	ENST00000367477.7	n.696-460T>C		intron_variant	Intron 8 of 10	2
STXBP5-AS1	ENST00000433308.2	n.436-460T>C		intron_variant	Intron 6 of 9	2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81706 AN: 151866 Hom.: 22058 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.538 AC: 81794 AN: 151986 Hom.: 22086 Cov.: 32 AF XY: 0.538 AC XY: 39987 AN XY: 74276

African (AFR) AF: 0.509 AC: 21078 AN: 41426

American (AMR) AF: 0.559 AC: 8547 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3691 AN: 5154

South Asian (SAS) AF: 0.550 AC: 2639 AN: 4802

European-Finnish (FIN) AF: 0.527 AC: 5565 AN: 10566

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37071 AN: 67976

Other (OTH) AF: 0.535 AC: 1128 AN: 2110

Alfa AF: 0.541 Hom.: 95579

Bravo AF: 0.540

Asia WGS AF: 0.626 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.48
DANN	Benign	0.63
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9322079; hg19: chr6-147182339;