chr2-172108100-G-C

Variant names:

• chr2-172108100-G-C
• rs2357322
• ENST00000448117.1:n.677-802G>C

Variant summary

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

The NR_126376.1(DLX2-DT):​n.677-802G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,268 control chromosomes in the GnomAD database, including 6,829 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 0.29 (6829 hom., cov: 33)
• Consequence: DLX2-DT NR_126376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126376.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX2-DT	NR_126376.1		n.677-802G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX2-DT	ENST00000448117.1	TSL:5	n.677-802G>C		intron	N/A
	DLX2-DT	ENST00000715288.1		n.242-802G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44305 AN: 152150 Hom.: 6822 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.291 AC: 44338 AN: 152268 Hom.: 6829 Cov.: 33 AF XY: 0.291 AC XY: 21688 AN XY: 74454

African (AFR) AF: 0.177 AC: 7355 AN: 41564

American (AMR) AF: 0.333 AC: 5099 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1102 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1036 AN: 5182

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4828

European-Finnish (FIN) AF: 0.376 AC: 3992 AN: 10606

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23361 AN: 68000

Other (OTH) AF: 0.294 AC: 621 AN: 2110

Alfa AF: 0.320 Hom.: 981

Bravo AF: 0.283

Asia WGS AF: 0.247 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.67
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2357322; hg19: chr2-172972828;