rs2933572

Variant names:

• chr4-4797965-G-A
• rs2933572
• ENST00000829246.1:n.764-22441G>A

Variant summary

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

The ENST00000829246.1(STX18-AS1):​n.764-22441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,068 control chromosomes in the GnomAD database, including 41,200 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 0.73 (41200 hom., cov: 32)
• Consequence: STX18-AS1 ENST00000829246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 3 publications found

Genes affected

STX18-AS1 (HGNC:48877): (STX18 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Benign. The variant received -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 = 0.849 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
STX18-AS1	ENST00000829246.1	n.764-22441G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111387 AN: 151950 Hom.: 41159 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.733 AC: 111476 AN: 152068 Hom.: 41200 Cov.: 32 AF XY: 0.733 AC XY: 54481 AN XY: 74322

African (AFR) AF: 0.811 AC: 33669 AN: 41498

American (AMR) AF: 0.627 AC: 9587 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4513 AN: 5184

South Asian (SAS) AF: 0.748 AC: 3604 AN: 4820

European-Finnish (FIN) AF: 0.743 AC: 7838 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47854 AN: 67952

Other (OTH) AF: 0.718 AC: 1515 AN: 2110

Alfa AF: 0.708 Hom.: 122402

Bravo AF: 0.725

Asia WGS AF: 0.804 AC: 2796 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	0.61
DANN	Benign	0.65
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2933572; hg19: chr4-4799692;