rs4689174

chr4-4577315-G-A

Variant summary

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

The XM_047416490.1(LOC124900165):c.-10127+32408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,076 control chromosomes in the GnomAD database, including 5,110 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 0.24 (5110 hom., cov: 32)
• Consequence: LOC124900165 XM_047416490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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 = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900165	XM_047416490.1	c.-10127+32408G>A		intron_variant
STX18-AS1	NR_037888.1	n.515+32408G>A		intron_variant, non_coding_transcript_variant
LINC03091	XR_007058000.1	n.66-2104C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STX18-AS1	ENST00000670162.1	n.454+32408G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36915 AN: 151960 Hom.: 5108 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.243 AC: 36930 AN: 152076 Hom.: 5110 Cov.: 32 AF XY: 0.248 AC XY: 18440 AN XY: 74326

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.252

Alfa AF: 0.278 Hom.: 12042

Bravo AF: 0.233

Asia WGS AF: 0.326 AC: 1132 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	1.3
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4689174; hg19: chr4-4579042;