dbSNP rs17410015: DPH5-DT:n.882-482T>C (chr1-101086370-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230

Publications

11 publications found

Variant links:

Genes affected

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

DPH5-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH5-DT	NR_109849.1 link	n.799-482T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DPH5-DT	ENST00000449473.2 link	n.882-482T>C	intron_variant	Intron 6 of 6	1
DPH5-DT	ENST00000446527.8 link	n.792-482T>C	intron_variant	Intron 4 of 4	3
DPH5-DT	ENST00000451213.2 link	n.3873-482T>C	intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.0608

AC:

9251

AN:

152136

Hom.:

379

Cov.:

show subpopulations

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.:

AF XY:

0.0581

AC XY:

4324

AN XY:

74446

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0878

AC:

5967

AN:

67980

Other (OTH)

AF:

0.0818

AC:

173

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

433

867

1300

1734

2167

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.5

(source)

DANN

Benign

0.74

PhyloP100

0.23

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over