chr7-96996807-G-T

Variant names:

• chr7-96996807-G-T
• rs6957108
• ENST00000458352.5:n.615+15018C>A

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+15018C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,056 control chromosomes in the GnomAD database, including 3,749 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 0.21 (3749 hom., cov: 31)
• Consequence: DLX6-AS1 ENST00000458352.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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+17118C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX6-AS1	ENST00000458352.5	TSL:1	n.615+15018C>A		intron	N/A
	DLX6-AS1	ENST00000430027.3	TSL:2	n.141+17118C>A		intron	N/A
	DLX6-AS1	ENST00000430404.7	TSL:4	n.58+15018C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32190 AN: 151938 Hom.: 3746 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.212 AC: 32224 AN: 152056 Hom.: 3749 Cov.: 31 AF XY: 0.207 AC XY: 15401 AN XY: 74346

African (AFR) AF: 0.307 AC: 12738 AN: 41456

American (AMR) AF: 0.169 AC: 2587 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.159 AC: 816 AN: 5142

South Asian (SAS) AF: 0.144 AC: 696 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10592

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12899 AN: 67968

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.200 Hom.: 4057

Bravo AF: 0.218

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6957108; hg19: chr7-96626119;