rs6446666

Positions:

• chr4-4592231-A-C
• chr4-4592231-A-G
• chr4-4592231-A-T

Variant summary

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

The XM_047416485.1(LOC124900165):​c.-9778+47324A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,994 control chromosomes in the GnomAD database, including 29,108 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 0.61 (29108 hom., cov: 32)
• Consequence: LOC124900165 XM_047416485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

STX18-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900165	XM_047416485.1	c.-9778+47324A>C		intron_variant			XP_047272441.1
LOC124900165	XM_047416486.1	c.-9775+47324A>C		intron_variant			XP_047272442.1
LOC124900165	XM_047416487.1	c.-10129-19263A>C		intron_variant			XP_047272443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000610009.5	n.442+47324A>C		intron_variant		1
STX18-AS1	ENST00000499430.7	n.604+47324A>C		intron_variant		2
STX18-AS1	ENST00000502693.1	n.358-45307A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93035 AN: 151876 Hom.: 29083 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.613 AC: 93115 AN: 151994 Hom.: 29108 Cov.: 32 AF XY: 0.609 AC XY: 45200 AN XY: 74280

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.594

Alfa AF: 0.524 Hom.: 4046

Bravo AF: 0.626

Asia WGS AF: 0.532 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6446666; hg19: chr4-4593958;