chr15-66288515-C-T

Variant names:

• chr15-66288515-C-T
• rs7170930
• ENST00000564269.2:n.167+4811G>A

Variant summary

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

The ENST00000564269.2(DIS3L-AS1):​n.167+4811G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,254 control chromosomes in the GnomAD database, including 391 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 0.065 (391 hom., cov: 32)
• Consequence: DIS3L-AS1 ENST00000564269.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 14 publications found

Genes affected

DIS3L-AS1 (HGNC:55369): (DIS3L antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.08 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564269.2. 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
	DIS3L-AS1	NR_183865.1		n.275-2328G>A		intron	N/A
	DIS3L-AS1	NR_183866.1		n.274+4711G>A		intron	N/A
	DIS3L-AS1	NR_183867.1		n.174+4811G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIS3L-AS1	ENST00000564269.2	TSL:2	n.167+4811G>A		intron	N/A
	DIS3L-AS1	ENST00000784663.1		n.265+4711G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0651 AC: 9906 AN: 152136 Hom.: 390 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0651 AC: 9910 AN: 152254 Hom.: 391 Cov.: 32 AF XY: 0.0633 AC XY: 4710 AN XY: 74430

African (AFR) AF: 0.0460 AC: 1910 AN: 41560

American (AMR) AF: 0.0555 AC: 848 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5190

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4830

European-Finnish (FIN) AF: 0.0694 AC: 734 AN: 10580

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5567 AN: 68018

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0596 Hom.: 119

Bravo AF: 0.0634

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.7
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7170930; hg19: chr15-66580853; COSMIC: COSV59913531;