rs3907154

Positions:

• chr18-67818052-G-A

Variant summary

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

The NR_033921.1(DSEL-AS1):​n.205-16367G>A variant causes a intron, non coding transcript 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 NR_033921.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSEL-AS1	NR_033921.1	n.205-16367G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000583687.1	n.205-16367G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.609

Alfa AF: 0.686 Hom.: 15052

Bravo AF: 0.592

Asia WGS AF: 0.809 AC: 2809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3907154; hg19: chr18-65485289;