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 XM_047416485.1(LOC124900165):​c.-9471-42779A>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: LOC124900165 XM_047416485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900165	XM_047416485.1	c.-9471-42779A>G		intron_variant	Intron 4 of 4		XP_047272441.1
LOC124900165	XM_047416486.1	c.-9471-42779A>G		intron_variant	Intron 4 of 4		XP_047272442.1
LOC124900165	XM_047416487.1	c.-9471-42779A>G		intron_variant	Intron 5 of 5		XP_047272443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000499430.7	n.1171-12060A>G		intron_variant	Intron 3 of 3	2
STX18-AS1	ENST00000653097.1	n.611-12060A>G		intron_variant	Intron 2 of 2
STX18-AS1	ENST00000655855.1	n.536-12060A>G		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.485 AC: 0.484952 AN: 0.484952

Gnomad4 AMR AF: 0.542 AC: 0.541579 AN: 0.541579

Gnomad4 ASJ AF: 0.344 AC: 0.34447 AN: 0.34447

Gnomad4 EAS AF: 0.570 AC: 0.569632 AN: 0.569632

Gnomad4 SAS AF: 0.531 AC: 0.531367 AN: 0.531367

Gnomad4 FIN AF: 0.356 AC: 0.356141 AN: 0.356141

Gnomad4 NFE AF: 0.407 AC: 0.407304 AN: 0.407304

Gnomad4 OTH AF: 0.457 AC: 0.456913 AN: 0.456913

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1000579; hg19: chr4-4719494;