rs10486860

chr7-96969514-C-T

Variant summary

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

The NR_015448.1(DLX6-AS1):n.1387-396G>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 0.0655 in 152,134 control chromosomes in the GnomAD database, including 533 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 (533 hom., cov: 32)
• Consequence: DLX6-AS1 NR_015448.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

DLX6-AS1 (HGNC:37151): (DLX6 antisense RNA 1) Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLX6-AS1	NR_015448.1	n.1387-396G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLX6-AS1	ENST00000430027.3	n.1387-396G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9954 AN: 152016 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0655 AC: 9962 AN: 152134 Hom.: 533 Cov.: 32 AF XY: 0.0679 AC XY: 5050 AN XY: 74378

Gnomad4 AFR AF: 0.0481

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0568

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0614 Hom.: 758

Bravo AF: 0.0653

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.16
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486860; hg19: chr7-96598826;