rs7170930

chr15-66288515-C-T

Variant summary

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

The NR_183867.1(DIS3L-AS1):n.174+4811G>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 0.0651 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 NR_183867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIS3L-AS1	NR_183867.1	n.174+4811G>A		intron_variant, non_coding_transcript_variant
DIS3L-AS1	NR_183865.1	n.275-2328G>A		intron_variant, non_coding_transcript_variant
DIS3L-AS1	NR_183866.1	n.274+4711G>A		intron_variant, non_coding_transcript_variant
DIS3L-AS1	NR_183868.1	n.175-2328G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIS3L-AS1	ENST00000564269.1	n.32+4811G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.0555

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.0818

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0541 Hom.: 54

Bravo AF: 0.0634

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.7
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

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