rs16835979

Variant names:

• chr4-4633549-C-A
• rs16835979
• ENST00000610009.5:n.443-15428C>A

Variant summary

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

The ENST00000610009.5(STX18-AS1):​n.443-15428C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,142 control chromosomes in the GnomAD database, including 3,493 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 0.21 (3493 hom., cov: 33)
• Consequence: STX18-AS1 ENST00000610009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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.516-15428C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STX18-AS1	ENST00000610009.5	TSL:1	n.443-15428C>A		intron	N/A
	STX18-AS1	ENST00000499430.7	TSL:2	n.605-15428C>A		intron	N/A
	STX18-AS1	ENST00000502693.1	TSL:3	n.358-3989C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31243 AN: 152024 Hom.: 3496 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.205 AC: 31251 AN: 152142 Hom.: 3493 Cov.: 33 AF XY: 0.209 AC XY: 15520 AN XY: 74372

African (AFR) AF: 0.113 AC: 4688 AN: 41530

American (AMR) AF: 0.210 AC: 3215 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1636 AN: 5176

South Asian (SAS) AF: 0.292 AC: 1405 AN: 4814

European-Finnish (FIN) AF: 0.231 AC: 2440 AN: 10578

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16402 AN: 67982

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.230 Hom.: 2327

Bravo AF: 0.197

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.68
DANN	Benign	0.51
PhyloP100		-0.98

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: rs16835979;

hg19: chr4-4635276;