rs3907154

Variant names:

• chr18-67818052-G-A
• rs3907154
• ENST00000583687.1:n.205-16367G>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.205-16367G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,844 control chromosomes in the GnomAD database, including 31,962 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 (31962 hom., cov: 33)
• Consequence: DSEL-AS1 ENST00000583687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• 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 (EAS) allele frequency at 95% confidence interval = 0.898 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.205-16367G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DSEL-AS1	ENST00000583687.1	TSL:1	n.205-16367G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93282 AN: 151726 Hom.: 31959 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.614 AC: 93299 AN: 151844 Hom.: 31962 Cov.: 33 AF XY: 0.629 AC XY: 46665 AN XY: 74232

African (AFR) AF: 0.302 AC: 12501 AN: 41438

American (AMR) AF: 0.718 AC: 10948 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1916 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4757 AN: 5172

South Asian (SAS) AF: 0.766 AC: 3696 AN: 4828

European-Finnish (FIN) AF: 0.866 AC: 9179 AN: 10596

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48210 AN: 67774

Other (OTH) AF: 0.609 AC: 1282 AN: 2106

Alfa AF: 0.682 Hom.: 15100

Bravo AF: 0.592

Asia WGS AF: 0.809 AC: 2809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.36

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: rs3907154;

hg19: chr18-65485289;