ENST00000610009.5:n.746-19763A>G

Variant names:

• chr4-4685910-A-G
• rs7694974
• ENST00000610009.5:n.746-19763A>G

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.746-19763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,006 control chromosomes in the GnomAD database, including 23,742 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 0.56 (23742 hom., cov: 33)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610009.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	NR_037888.1		n.819-19763A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	ENST00000610009.5	TSL:1	n.746-19763A>G		intron	N/A
	STX18-AS1	ENST00000499430.7	TSL:2	n.1170+36368A>G		intron	N/A
	STX18-AS1	ENST00000608184.2	TSL:3	n.742-19763A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84430 AN: 151888 Hom.: 23720 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.556 AC: 84491 AN: 152006 Hom.: 23742 Cov.: 33 AF XY: 0.556 AC XY: 41307 AN XY: 74290

African (AFR) AF: 0.621 AC: 25764 AN: 41472

American (AMR) AF: 0.518 AC: 7911 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2729 AN: 5156

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6480 AN: 10584

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36132 AN: 67928

Other (OTH) AF: 0.522 AC: 1103 AN: 2112

Alfa AF: 0.526 Hom.: 10768

Bravo AF: 0.552

Asia WGS AF: 0.531 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.0
DANN	Benign	0.28
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7694974; hg19: chr4-4687637;