rs2357322

Positions:

• chr2-172108100-G-C

Variant summary

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

The NR_126376.1(DLX2-DT):​n.677-802G>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 0.291 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLX2-DT	NR_126376.1	n.677-802G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLX2-DT	ENST00000448117.1	n.677-802G>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.294

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357322; hg19: chr2-172972828;