rs16835979

Positions:

• chr4-4633549-C-A

Variant summary

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

The XM_047416490.1(LOC124900165):​c.-9774-15428C>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: LOC124900165 XM_047416490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983

Genes affected

LOC124900165 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900165	XM_047416490.1	c.-9774-15428C>A		intron_variant			XP_047272446.1
STX18-AS1	NR_037888.1	n.516-15428C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STX18-AS1	ENST00000670162.1	n.455-15428C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.211

Alfa AF: 0.231 Hom.: 2112

Bravo AF: 0.197

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16835979; hg19: chr4-4635276;