4-4612553-C-T

Variant names:

• chr4-4612553-C-T
• rs6824295
• ENST00000610009.5:n.443-36424C>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.443-36424C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,208 control chromosomes in the GnomAD database, including 3,581 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 0.21 (3581 hom., cov: 32)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STX18-AS1	NR_037888.1	n.516-36424C>T		intron_variant	Intron 2 of 5
LOC124900165	XM_047416485.1	c.-9777-36424C>T		intron_variant	Intron 2 of 4		XP_047272441.1
LOC124900165	XM_047416486.1	c.-9774-36424C>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.443-36424C>T		intron_variant	Intron 2 of 5	1
STX18-AS1	ENST00000499430.7	n.605-36424C>T		intron_variant	Intron 2 of 3	2
STX18-AS1	ENST00000502693.1	n.358-24985C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31597 AN: 152088 Hom.: 3584 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.208 AC: 31597 AN: 152208 Hom.: 3581 Cov.: 32 AF XY: 0.211 AC XY: 15707 AN XY: 74400

African (AFR) AF: 0.116 AC: 4828 AN: 41568

American (AMR) AF: 0.211 AC: 3235 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 591 AN: 3466

East Asian (EAS) AF: 0.334 AC: 1726 AN: 5164

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2492 AN: 10584

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16453 AN: 67986

Other (OTH) AF: 0.210 AC: 444 AN: 2116

Alfa AF: 0.217 Hom.: 2608

Bravo AF: 0.198

Asia WGS AF: 0.289 AC: 1004 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	0.040
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6824295; hg19: chr4-4614280;