dbSNP rs7187476: ENKD1:c.280+26A>G (chr16-67666045-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 NM_032140.3(ENKD1):c.280+26A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,605,300 control chromosomes in the GnomAD database, including 36,489 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 0.30 ( 10208 hom., cov: 33)

Exomes 𝑓: 0.17 ( 26281 hom. )

Consequence

ENKD1
NM_032140.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107

Publications

28 publications found

Variant links:

Genes affected

ENKD1 (HGNC:25246): (enkurin domain containing 1) Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENKD1 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032140.3. 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
	ENKD1	NM_032140.3	MANE Select	c.280+26A>G		intron	N/A	NP_115516.1
	ENKD1	NR_138150.2		n.588+26A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENKD1	ENST00000243878.9	TSL:1 MANE Select	c.280+26A>G	intron	N/A	ENSP00000243878.4
ENKD1	ENST00000602644.5	TSL:5	c.280+26A>G	intron	N/A	ENSP00000473501.1
ENKD1	ENST00000602409.2	TSL:3	c.58+26A>G	intron	N/A	ENSP00000483290.1

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45069

AN:

152050

Hom.:

10172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.0293

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.264

GnomAD2 exomes

AF:

0.198

AC:

47794

AN:

240986

AF XY:

0.192

show subpopulations

Gnomad AFR exome

AF:

0.640

Gnomad AMR exome

AF:

0.197

Gnomad ASJ exome

AF:

0.157

Gnomad EAS exome

AF:

0.0243

Gnomad FIN exome

AF:

0.180

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.186

GnomAD4 exome

AF:

0.169

AC:

246251

AN:

1453132

Hom.:

26281

Cov.:

AF XY:

0.171

AC XY:

123241

AN XY:

722212

show subpopulations

African (AFR)

AF:

0.652

AC:

21357

AN:

32748

American (AMR)

AF:

0.204

AC:

8979

AN:

44004

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

4224

AN:

25892

East Asian (EAS)

AF:

0.0341

AC:

1346

AN:

39482

South Asian (SAS)

AF:

0.244

AC:

20980

AN:

85818

European-Finnish (FIN)

AF:

0.180

AC:

9340

AN:

52020

Middle Eastern (MID)

AF:

0.238

AC:

1362

AN:

5732

European-Non Finnish (NFE)

AF:

0.151

AC:

167301

AN:

1107452

Other (OTH)

AF:

0.189

AC:

11362

AN:

59984

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

10121

20242

30364

40485

50606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6160

12320

18480

24640

30800

<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:

0.297

AC:

45156

AN:

152168

Hom.:

10208

Cov.:

AF XY:

0.294

AC XY:

21878

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.634

AC:

26334

AN:

41506

American (AMR)

AF:

0.231

AC:

3536

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

563

AN:

3470

East Asian (EAS)

AF:

0.0295

AC:

153

AN:

5178

South Asian (SAS)

AF:

0.238

AC:

1146

AN:

4824

European-Finnish (FIN)

AF:

0.185

AC:

1963

AN:

10598

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10694

AN:

67988

Other (OTH)

AF:

0.265

AC:

560

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1329

2658

3987

5316

6645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.187

Hom.:

3391

Bravo

AF:

0.310

Asia WGS

AF:

0.214

AC:

746

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.7

(source)

DANN

Benign

0.62

PhyloP100

-0.11

PromoterAI

0.027

Neutral

(source)

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