rs4689174

Variant names:

• chr4-4577315-G-A
• rs4689174
• ENST00000610009.5:n.442+32408G>A

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.442+32408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,076 control chromosomes in the GnomAD database, including 5,110 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 0.24 (5110 hom., cov: 32)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 5 publications found

Genes affected

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

ENSG00000307864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX18-AS1	NR_037888.1	n.515+32408G>A		intron_variant	Intron 2 of 5
LOC124900165	XM_047416485.1	c.-9778+32408G>A		intron_variant	Intron 2 of 4		XP_047272441.1
LOC124900165	XM_047416486.1	c.-9775+32408G>A		intron_variant	Intron 2 of 4		XP_047272442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000610009.5	n.442+32408G>A		intron_variant	Intron 2 of 5	1
STX18-AS1	ENST00000499430.7	n.604+32408G>A		intron_variant	Intron 2 of 3	2
STX18-AS1	ENST00000502693.1	n.357+32408G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36915 AN: 151960 Hom.: 5108 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.243 AC: 36930 AN: 152076 Hom.: 5110 Cov.: 32 AF XY: 0.248 AC XY: 18440 AN XY: 74326

African (AFR) AF: 0.108 AC: 4498 AN: 41522

American (AMR) AF: 0.269 AC: 4120 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1884 AN: 5156

South Asian (SAS) AF: 0.292 AC: 1405 AN: 4810

European-Finnish (FIN) AF: 0.364 AC: 3840 AN: 10562

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.289 AC: 19631 AN: 67956

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.272 Hom.: 24816

Bravo AF: 0.233

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs4689174; hg19: chr4-4579042;