7-96995967-T-G

Position:

• chr7-96995967-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_015448.1(DLX6-AS1):​n.142-16376A>C variant causes a intron, non coding transcript 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 NR_015448.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DLX6-AS1	NR_015448.1	n.142-16376A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX6-AS1	ENST00000430027.3	n.142-16376A>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.961

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886583; hg19: chr7-96625279;