rs75687134

Variant names:

• chr18-67804806-G-A
• rs75687134
• ENST00000583687.1:n.205-29613G>A

Variant summary

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

The ENST00000583687.1(DSEL-AS1):​n.205-29613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0495 in 152,256 control chromosomes in the GnomAD database, including 234 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 0.050 (234 hom., cov: 32)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 1 publications found

Genes affected

DSEL-AS1 (HGNC:55325): (DSEL antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583687.1. 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
	DSEL-AS1	NR_033921.1		n.205-29613G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DSEL-AS1	ENST00000583687.1	TSL:1	n.205-29613G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7531 AN: 152138 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0495 AC: 7540 AN: 152256 Hom.: 234 Cov.: 32 AF XY: 0.0475 AC XY: 3536 AN XY: 74454

African (AFR) AF: 0.0498 AC: 2069 AN: 41540

American (AMR) AF: 0.0519 AC: 794 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4826

European-Finnish (FIN) AF: 0.0123 AC: 131 AN: 10616

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3573 AN: 68010

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0495 Hom.: 60

Bravo AF: 0.0513

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		-0.39

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: rs75687134;

hg19: chr18-65472043;