7-96995967-T-G

Variant names:

• chr7-96995967-T-G
• rs886583
• ENST00000458352.5:n.615+15858A>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+15858A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 144,932 control chromosomes in the GnomAD database, including 66,207 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 (66207 hom., cov: 25)
• Consequence: DLX6-AS1 ENST00000458352.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408
• Publications: 1 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 = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLX6-AS1	NR_015448.1	n.142-16376A>C		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+15858A>C		intron_variant	Intron 2 of 3	1
DLX6-AS1	ENST00000430027.3	n.142-16376A>C		intron_variant	Intron 1 of 2	2
DLX6-AS1	ENST00000430404.7	n.58+15858A>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.955 AC: 138375 AN: 144826 Hom.: 66152 Cov.: 25

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.993

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.956 AC: 138483 AN: 144932 Hom.: 66207 Cov.: 25 AF XY: 0.956 AC XY: 67430 AN XY: 70524

African (AFR) AF: 0.988 AC: 38922 AN: 39380

American (AMR) AF: 0.974 AC: 13966 AN: 14342

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3264 AN: 3356

East Asian (EAS) AF: 1.00 AC: 4888 AN: 4890

South Asian (SAS) AF: 0.974 AC: 4440 AN: 4560

European-Finnish (FIN) AF: 0.917 AC: 8911 AN: 9720

Middle Eastern (MID) AF: 0.993 AC: 276 AN: 278

European-Non Finnish (NFE) AF: 0.932 AC: 61075 AN: 65534

Other (OTH) AF: 0.961 AC: 1926 AN: 2004

Alfa AF: 0.942 Hom.: 8361

Bravo AF: 0.963

Asia WGS AF: 0.986 AC: 3270 AN: 3316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.44
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs886583; hg19: chr7-96625279;