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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ENKD1	NM_032140.3 link	c.280+26A>G	intron_variant	Intron 2 of 6	ENST00000243878.9	NP_115516.1	Q9H0I2-1
ENKD1	NR_138150.2 link	n.588+26A>G	intron_variant	Intron 2 of 5
ENKD1	XM_024450469.2 link	c.280+26A>G	intron_variant	Intron 2 of 5		XP_024306237.1
ENKD1	XM_024450470.2 link	c.280+26A>G	intron_variant	Intron 2 of 5		XP_024306238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENKD1	ENST00000243878.9 link	c.280+26A>G		intron_variant	Intron 2 of 6	1	NM_032140.3	ENSP00000243878.4		Q9H0I2-1

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

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

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 v4.3

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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rs7187476

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over