rs4476553

Variant names:

• chr4-4702287-C-T
• rs4476553
• ENST00000610009.5:n.746-3386C>T

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.746-3386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,018 control chromosomes in the GnomAD database, including 27,227 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 0.59 (27227 hom., cov: 32)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 2 publications found

Genes affected

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

LOC124900165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX18-AS1	NR_037888.1	n.819-3386C>T		intron_variant	Intron 4 of 5
LOC124900165	XM_047416485.1	c.-9472+52745C>T		intron_variant	Intron 4 of 4		XP_047272441.1
LOC124900165	XM_047416486.1	c.-9472+52745C>T		intron_variant	Intron 4 of 4		XP_047272442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000610009.5	n.746-3386C>T		intron_variant	Intron 4 of 5	1
STX18-AS1	ENST00000499430.7	n.1171-27540C>T		intron_variant	Intron 3 of 3	2
STX18-AS1	ENST00000608184.2	n.742-3386C>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89742 AN: 151900 Hom.: 27194 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.591 AC: 89821 AN: 152018 Hom.: 27227 Cov.: 32 AF XY: 0.591 AC XY: 43891 AN XY: 74296

African (AFR) AF: 0.731 AC: 30343 AN: 41490

American (AMR) AF: 0.531 AC: 8104 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1704 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2738 AN: 5152

South Asian (SAS) AF: 0.406 AC: 1953 AN: 4814

European-Finnish (FIN) AF: 0.616 AC: 6503 AN: 10550

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.539 AC: 36663 AN: 67960

Other (OTH) AF: 0.545 AC: 1151 AN: 2112

Alfa AF: 0.546 Hom.: 59858

Bravo AF: 0.592

Asia WGS AF: 0.533 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.85
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs4476553; hg19: chr4-4704014;