7-97001325-A-G

Position:

• chr7-97001325-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

DLX6-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX6-AS1	NR_015448.1	n.141+12600T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX6-AS1	ENST00000458352.5	n.615+10500T>C		intron_variant		1
DLX6-AS1	ENST00000430027.3	n.141+12600T>C		intron_variant		2
DLX6-AS1	ENST00000430404.7	n.58+10500T>C		intron_variant		4

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

Gnomad4 AFR AF: 0.0755

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.288

Alfa AF: 0.295 Hom.: 3023

Bravo AF: 0.238

Asia WGS AF: 0.317 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11762736; hg19: chr7-96630637;