18-67928612-C-T

Variant names:

• chr18-67928612-C-T
• rs1350744
• ENST00000757632.1:n.665-895C>T

Variant summary

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

The ENST00000757632.1(DSEL-AS1):​n.665-895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,164 control chromosomes in the GnomAD database, including 65,738 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 0.92 (65738 hom., cov: 33)
• Consequence: DSEL-AS1 ENST00000757632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSEL-AS1	ENST00000757632.1	n.665-895C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140527 AN: 152046 Hom.: 65703 Cov.: 33

Gnomad AFR AF: 0.758

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.975

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.924 AC: 140624 AN: 152164 Hom.: 65738 Cov.: 33 AF XY: 0.927 AC XY: 68941 AN XY: 74390

African (AFR) AF: 0.758 AC: 31437 AN: 41472

American (AMR) AF: 0.966 AC: 14762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3433 AN: 3472

East Asian (EAS) AF: 0.952 AC: 4932 AN: 5180

South Asian (SAS) AF: 0.975 AC: 4701 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10615 AN: 10616

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67550 AN: 67992

Other (OTH) AF: 0.943 AC: 1995 AN: 2116

Alfa AF: 0.941 Hom.: 7829

Bravo AF: 0.913

Asia WGS AF: 0.962 AC: 3310 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.7
DANN	Benign	0.46
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1350744; hg19: chr18-65595849;