rs1989223

Variant names:

• chr15-35834905-T-C
• rs1989223
• ENST00000501169.3:n.504-23082T>C

Variant summary

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

The ENST00000501169.3(DPH6-DT):​n.504-23082T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,212 control chromosomes in the GnomAD database, including 3,746 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 0.21 (3746 hom., cov: 33)
• Consequence: DPH6-DT ENST00000501169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 5 publications found

Genes affected

DPH6-DT (HGNC:44147): (DPH6 divergent transcript)

ENSG00000306727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501169.3. 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
	DPH6-DT	NR_038251.1		n.463-23082T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPH6-DT	ENST00000501169.3	TSL:1	n.504-23082T>C		intron	N/A
	DPH6-DT	ENST00000559210.1	TSL:3	n.177-23082T>C		intron	N/A
	DPH6-DT	ENST00000661846.2		n.402-22217T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31700 AN: 152094 Hom.: 3748 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152212 Hom.: 3746 Cov.: 33 AF XY: 0.212 AC XY: 15737 AN XY: 74404

African (AFR) AF: 0.0917 AC: 3809 AN: 41550

American (AMR) AF: 0.181 AC: 2769 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.191 AC: 988 AN: 5174

South Asian (SAS) AF: 0.277 AC: 1337 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3316 AN: 10596

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17743 AN: 67990

Other (OTH) AF: 0.215 AC: 455 AN: 2116

Alfa AF: 0.240 Hom.: 2669

Bravo AF: 0.188

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs1989223; hg19: chr15-36127106;