rs11762736

Variant names:

• chr7-97001325-A-G
• rs11762736
• ENST00000458352.5:n.615+10500T>C

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+10500T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,178 control chromosomes in the GnomAD database, including 6,791 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 0.27 (6791 hom., cov: 33)
• Consequence: DLX6-AS1 ENST00000458352.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458352.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6-AS1	NR_015448.1		n.141+12600T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6-AS1	ENST00000458352.5	TSL:1	n.615+10500T>C		intron	N/A
	DLX6-AS1	ENST00000430027.3	TSL:2	n.141+12600T>C		intron	N/A
	DLX6-AS1	ENST00000430404.7	TSL:4	n.58+10500T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40802 AN: 152062 Hom.: 6802 Cov.: 33

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.268 AC: 40776 AN: 152178 Hom.: 6791 Cov.: 33 AF XY: 0.274 AC XY: 20395 AN XY: 74392

African (AFR) AF: 0.0755 AC: 3136 AN: 41558

American (AMR) AF: 0.207 AC: 3172 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1569 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1817 AN: 4812

European-Finnish (FIN) AF: 0.443 AC: 4693 AN: 10584

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24230 AN: 67990

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.269 Hom.: 5798

Bravo AF: 0.238

Asia WGS AF: 0.317 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.040
DANN	Benign	0.47
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11762736; hg19: chr7-96630637;