rs17410015

Variant names:

• chr1-101086370-T-C
• rs17410015
• ENST00000449473.2:n.882-482T>C

Variant summary

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

The ENST00000449473.2(DPH5-DT):​n.882-482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 152,254 control chromosomes in the GnomAD database, including 381 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 0.061 (381 hom., cov: 32)
• Consequence: DPH5-DT ENST00000449473.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 11 publications found

Genes affected

DPH5-DT (HGNC:53720): (DPH5 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449473.2. 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
	DPH5-DT	NR_109849.1		n.799-482T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPH5-DT	ENST00000449473.2	TSL:1	n.882-482T>C		intron	N/A
	DPH5-DT	ENST00000446527.8	TSL:3	n.792-482T>C		intron	N/A
	DPH5-DT	ENST00000451213.2	TSL:2	n.3873-482T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9251 AN: 152136 Hom.: 379 Cov.: 32

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0608 AC: 9251 AN: 152254 Hom.: 381 Cov.: 32 AF XY: 0.0581 AC XY: 4324 AN XY: 74446

African (AFR) AF: 0.0177 AC: 737 AN: 41570

American (AMR) AF: 0.0702 AC: 1074 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3466

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5186

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4824

European-Finnish (FIN) AF: 0.0438 AC: 465 AN: 10614

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5967 AN: 67980

Other (OTH) AF: 0.0818 AC: 173 AN: 2114

Alfa AF: 0.0797 Hom.: 1672

Bravo AF: 0.0609

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17410015;

hg19: chr1-101551926;