rs1005169

Variant names:

• chr7-97013613-A-C
• rs1005169
• ENST00000458352.5:n.136+312T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-97013613-A-C
• chr7-97013613-A-G
• chr7-97013613-A-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.136+312T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 152,224 control chromosomes in the GnomAD database, including 70,688 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 0.96 (70688 hom., cov: 31)
• Consequence: DLX6-AS1 ENST00000458352.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.67
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6-AS1	NR_015448.1		n.141+312T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6-AS1	ENST00000458352.5	TSL:1	n.136+312T>G		intron	N/A
	DLX6-AS1	ENST00000685183.2		n.448T>G		non_coding_transcript_exon	Exon 1 of 1
	DLX6-AS1	ENST00000430027.3	TSL:2	n.141+312T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.963 AC: 146534 AN: 152106 Hom.: 70627 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.982

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.963 AC: 146654 AN: 152224 Hom.: 70688 Cov.: 31 AF XY: 0.963 AC XY: 71688 AN XY: 74420

African (AFR) AF: 0.991 AC: 41181 AN: 41540

American (AMR) AF: 0.982 AC: 15027 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3277 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5124 AN: 5150

South Asian (SAS) AF: 0.977 AC: 4703 AN: 4816

European-Finnish (FIN) AF: 0.929 AC: 9857 AN: 10614

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64289 AN: 68014

Other (OTH) AF: 0.969 AC: 2045 AN: 2110

Alfa AF: 0.954 Hom.: 26695

Bravo AF: 0.969

Asia WGS AF: 0.987 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0060
DANN	Benign	0.37
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs1005169; hg19: chr7-96642925;