rs1650146

chr10-77928450-A-Gchr10-77928450-A-T

Variant summary

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

The NR_024585.1(DLG5-AS1):n.1639A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,202 control chromosomes in the GnomAD database, including 40,737 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 0.72 (40721 hom., cov: 32)
  • Exomes 𝑓: 0.66 (16 hom.)
• Consequence: DLG5-AS1 NR_024585.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856

Genes affected

DLG5-AS1 (HGNC:45109): (DLG5 antisense RNA 1)

DLG5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLG5-AS1	NR_024585.1	n.1639A>G		non_coding_transcript_exon_variant	1/1
DLG5	XM_047425998.1	c.-27+12220T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLG5-AS1	ENST00000449852.1	n.251+828A>G		intron_variant, non_coding_transcript_variant		2
DLG5-AS1	ENST00000632919.1	n.820A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109201 AN: 152020 Hom.: 40659 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.694

GnomAD4 exome AF: 0.656 AC: 42 AN: 64 Hom.: 16 Cov.: 0 AF XY: 0.646 AC XY: 31 AN XY: 48

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.750

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.640

GnomAD4 genome AF: 0.719 AC: 109324 AN: 152138 Hom.: 40721 Cov.: 32 AF XY: 0.715 AC XY: 53175 AN XY: 74356

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.695

Alfa AF: 0.675 Hom.: 8597

Bravo AF: 0.740

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.2
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1650146; hg19: chr10-79688208;