rs1000579

Variant names:

• chr4-4717767-A-G
• rs1000579
• XM_047416485.1:c.-9471-42779A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-4717767-A-G
• chr4-4717767-A-T

Variant summary

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

The ENST00000499430.7(STX18-AS1):​n.1171-12060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,030 control chromosomes in the GnomAD database, including 15,539 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 0.45 (15539 hom., cov: 33)
• Consequence: STX18-AS1 ENST00000499430.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 15 publications found

Genes affected

LOC124900165 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499430.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	ENST00000499430.7	TSL:2	n.1171-12060A>G		intron	N/A
	STX18-AS1	ENST00000653097.1		n.611-12060A>G		intron	N/A
	STX18-AS1	ENST00000655855.1		n.536-12060A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67820 AN: 151912 Hom.: 15509 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.447 AC: 67891 AN: 152030 Hom.: 15539 Cov.: 33 AF XY: 0.447 AC XY: 33248 AN XY: 74306

African (AFR) AF: 0.485 AC: 20110 AN: 41468

American (AMR) AF: 0.542 AC: 8271 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1196 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2945 AN: 5170

South Asian (SAS) AF: 0.531 AC: 2558 AN: 4814

European-Finnish (FIN) AF: 0.356 AC: 3758 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27682 AN: 67964

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.434 Hom.: 52061

Bravo AF: 0.462

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1000579;

hg19: chr4-4719494;