ENST00000610009.5:n.443-2657C>T

Variant names:

• chr4-4646320-C-T
• rs870142
• ENST00000610009.5:n.443-2657C>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.443-2657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,110 control chromosomes in the GnomAD database, including 3,307 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 0.20 (3307 hom., cov: 31)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 27 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX18-AS1	NR_037888.1	n.516-2657C>T		intron_variant	Intron 2 of 5
LOC124900165	XM_047416485.1	c.-9777-2657C>T		intron_variant	Intron 2 of 4		XP_047272441.1
LOC124900165	XM_047416486.1	c.-9774-2657C>T		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.443-2657C>T		intron_variant	Intron 2 of 5	1
STX18-AS1	ENST00000499430.7	n.605-2657C>T		intron_variant	Intron 2 of 3	2
STX18-AS1	ENST00000608184.2	n.436-2657C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29874 AN: 151992 Hom.: 3309 Cov.: 31

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.196 AC: 29873 AN: 152110 Hom.: 3307 Cov.: 31 AF XY: 0.200 AC XY: 14866 AN XY: 74368

African (AFR) AF: 0.0868 AC: 3604 AN: 41508

American (AMR) AF: 0.205 AC: 3139 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1604 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1371 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2496 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16325 AN: 67972

Other (OTH) AF: 0.206 AC: 434 AN: 2106

Alfa AF: 0.215 Hom.: 7006

Bravo AF: 0.186

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs870142; hg19: chr4-4648047;