rs17657924

chr7-96996277-C-Achr7-96996277-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.142-16686G>T 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 0.358 in 151,624 control chromosomes in the GnomAD database, including 11,419 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 0.36 (11419 hom., cov: 30)
• Consequence: DLX6-AS1 NR_015448.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLX6-AS1	NR_015448.1	n.142-16686G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLX6-AS1	ENST00000430027.3	n.142-16686G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54319 AN: 151510 Hom.: 11428 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.358 AC: 54315 AN: 151624 Hom.: 11419 Cov.: 30 AF XY: 0.364 AC XY: 26964 AN XY: 74064

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.375

Alfa AF: 0.435 Hom.: 16754

Bravo AF: 0.329

Asia WGS AF: 0.381 AC: 1321 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	3.4
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17657924; hg19: chr7-96625589;