7-96996277-C-A

Variant names:

• chr7-96996277-C-A
• rs17657924
• ENST00000458352.5:n.615+15548G>T

Variant summary

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

The ENST00000458352.5(DLX6-AS1):​n.615+15548G>T variant causes a intron 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 ENST00000458352.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DLX6-AS1	NR_015448.1	n.142-16686G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLX6-AS1	ENST00000458352.5	n.615+15548G>T		intron_variant	Intron 2 of 3	1
DLX6-AS1	ENST00000430027.3	n.142-16686G>T		intron_variant	Intron 1 of 2	2
DLX6-AS1	ENST00000430404.7	n.58+15548G>T		intron_variant	Intron 1 of 2	4

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

African (AFR) AF: 0.134 AC: 5556 AN: 41396

American (AMR) AF: 0.323 AC: 4922 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1749 AN: 3456

East Asian (EAS) AF: 0.359 AC: 1827 AN: 5092

South Asian (SAS) AF: 0.462 AC: 2218 AN: 4796

European-Finnish (FIN) AF: 0.556 AC: 5832 AN: 10496

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30965 AN: 67832

Other (OTH) AF: 0.375 AC: 790 AN: 2108

Alfa AF: 0.419 Hom.: 37516

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17657924; hg19: chr7-96625589;