chr2-172108243-G-A

Variant names:

• chr2-172108243-G-A
• rs2016394
• ENST00000448117.1:n.677-659G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448117.1(DLX2-DT):​n.677-659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,168 control chromosomes in the GnomAD database, including 12,837 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 0.40 (12837 hom., cov: 34)
• Consequence: DLX2-DT ENST00000448117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 80 publications found

Genes affected

DLX2-DT (HGNC:50638): (DLX2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448117.1. 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
	DLX2-DT	NR_126376.1		n.677-659G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX2-DT	ENST00000448117.1	TSL:5	n.677-659G>A		intron	N/A
	DLX2-DT	ENST00000715288.1		n.242-659G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60784 AN: 152048 Hom.: 12823 Cov.: 34

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.400 AC: 60829 AN: 152168 Hom.: 12837 Cov.: 34 AF XY: 0.397 AC XY: 29559 AN XY: 74388

African (AFR) AF: 0.271 AC: 11253 AN: 41536

American (AMR) AF: 0.423 AC: 6475 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1028 AN: 5160

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5367 AN: 10602

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32070 AN: 67954

Other (OTH) AF: 0.411 AC: 868 AN: 2114

Alfa AF: 0.455 Hom.: 29171

Bravo AF: 0.388

Asia WGS AF: 0.274 AC: 955 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.84
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2016394; hg19: chr2-172972971;