rs6818421

Positions:

• chr4-4687835-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047416485.1(LOC124900165):​c.-9472+38293A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,970 control chromosomes in the GnomAD database, including 23,708 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 (23708 hom., cov: 32)
• Consequence: LOC124900165 XM_047416485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

Genes affected

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

LOC124900165 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900165	XM_047416485.1	c.-9472+38293A>C		intron_variant			XP_047272441.1
LOC124900165	XM_047416486.1	c.-9472+38293A>C		intron_variant			XP_047272442.1
LOC124900165	XM_047416487.1	c.-9472+38293A>C		intron_variant			XP_047272443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000610009.5	n.746-17838A>C		intron_variant		1
STX18-AS1	ENST00000665126.1	n.633A>C		non_coding_transcript_exon_variant	4/5
STX18-AS1	ENST00000499430.7	n.1170+38293A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84348 AN: 151854 Hom.: 23686 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.555 AC: 84409 AN: 151970 Hom.: 23708 Cov.: 32 AF XY: 0.556 AC XY: 41265 AN XY: 74272

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.521

Alfa AF: 0.526 Hom.: 9176

Bravo AF: 0.552

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6818421; hg19: chr4-4689562;