4-4592231-A-C

Variant names:

• chr4-4592231-A-C
• rs6446666
• ENST00000610009.5:n.442+47324A>C

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.442+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: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610009.5. 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
	STX18-AS1	NR_037888.1		n.515+47324A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	ENST00000610009.5	TSL:1	n.442+47324A>C		intron	N/A
	STX18-AS1	ENST00000499430.7	TSL:2	n.604+47324A>C		intron	N/A
	STX18-AS1	ENST00000502693.1	TSL:3	n.358-45307A>C		intron	N/A

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

African (AFR) AF: 0.735 AC: 30484 AN: 41452

American (AMR) AF: 0.623 AC: 9512 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3205 AN: 5174

South Asian (SAS) AF: 0.516 AC: 2484 AN: 4814

European-Finnish (FIN) AF: 0.526 AC: 5546 AN: 10544

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38325 AN: 67974

Other (OTH) AF: 0.594 AC: 1247 AN: 2100

Alfa AF: 0.564 Hom.: 12108

Bravo AF: 0.626

Asia WGS AF: 0.532 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		-0.43

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: rs6446666;

hg19: chr4-4593958;