dbSNP rs1054442: DDN:c.*1203T>G (chr12-48995537-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015086.2(DDN):c.*1203T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,290 control chromosomes in the GnomAD database, including 16,555 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 0.45 ( 16540 hom., cov: 33)

Exomes 𝑓: 0.43 ( 15 hom. )

Consequence

DDN
NM_015086.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118

Publications

28 publications found

Variant links:

Genes affected

DDN (HGNC:24458): (dendrin) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in cell projection and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DDN links:

ENSG00000258283 (HGNC:):

ENSG00000258283 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015086.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDN	NM_015086.2	MANE Select	c.*1203T>G		3_prime_UTR	Exon 2 of 2	NP_055901.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDN	ENST00000421952.3	TSL:1 MANE Select	c.*1203T>G		3_prime_UTR	Exon 2 of 2	ENSP00000390590.2
	ENSG00000258283	ENST00000549516.1	TSL:3	n.205+183A>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68689

AN:

152022

Hom.:

16504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.389

GnomAD4 exome

AF:

0.433

AC:

AN:

150

Hom.:

Cov.:

AF XY:

0.445

AC XY:

AN XY:

110

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.405

AC:

AN:

126

Other (OTH)

AF:

0.417

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.452

AC:

68780

AN:

152140

Hom.:

16540

Cov.:

AF XY:

0.452

AC XY:

33596

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.622

AC:

25835

AN:

41504

American (AMR)

AF:

0.354

AC:

5422

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

1049

AN:

3472

East Asian (EAS)

AF:

0.424

AC:

2192

AN:

5166

South Asian (SAS)

AF:

0.506

AC:

2442

AN:

4824

European-Finnish (FIN)

AF:

0.433

AC:

4591

AN:

10594

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25896

AN:

67966

Other (OTH)

AF:

0.388

AC:

817

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1915

3831

5746

7662

9577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.388

Hom.:

19007

Bravo

AF:

0.444

Asia WGS

AF:

0.461

AC:

1603

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

9.2

(source)

DANN

Benign

0.35

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over