rs1005169

Positions:

• chr7-97013613-A-C
• chr7-97013613-A-G
• chr7-97013613-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

DLX6-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLX6-AS1	NR_015448.1	n.141+312T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLX6-AS1	ENST00000458352.5	n.136+312T>G		intron_variant		1
DLX6-AS1	ENST00000430027.3	n.141+312T>G		intron_variant		2
DLX6-AS1	ENST00000437331.4	n.136+312T>G		intron_variant		3

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

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.982

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.969

Alfa AF: 0.953 Hom.: 21338

Bravo AF: 0.969

Asia WGS AF: 0.987 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1005169; hg19: chr7-96642925;