dbSNP rs7717355: ANKDD1B:p.Thr315Thr (chr5-75656076-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001276713.2(ANKDD1B):c.945G>A(p.Thr315Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,526,186 control chromosomes in the GnomAD database, including 9,935 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 0.11 ( 1044 hom., cov: 32)

Exomes 𝑓: 0.11 ( 8891 hom. )

Consequence

ANKDD1B
NM_001276713.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.53

Publications

14 publications found

Variant links:

Genes affected

ANKDD1B (HGNC:32525): (ankyrin repeat and death domain containing 1B) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ANKDD1B Gene-Disease associations (from GenCC):

ankylosing spondylitis
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ANKDD1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.012).

BP7

Synonymous conserved (PhyloP=-5.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKDD1B	NM_001276713.2 link	c.945G>A	p.Thr315Thr	synonymous_variant	Exon 9 of 14	ENST00000601380.4	NP_001263642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKDD1B	ENST00000601380.4 link	c.945G>A	p.Thr315Thr	synonymous_variant	Exon 9 of 14	5	NM_001276713.2	ENSP00000471417.1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16550

AN:

151960

Hom.:

1044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0731

Gnomad AMI

AF:

0.0538

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0971

Gnomad OTH

AF:

0.115

GnomAD2 exomes

AF:

0.139

AC:

19094

AN:

137416

AF XY:

0.137

show subpopulations

Gnomad AFR exome

AF:

0.0700

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.0983

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.107

AC:

146425

AN:

1374108

Hom.:

8891

Cov.:

AF XY:

0.108

AC XY:

72994

AN XY:

678520

show subpopulations

African (AFR)

AF:

0.0732

AC:

2294

AN:

31342

American (AMR)

AF:

0.173

AC:

6137

AN:

35384

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

4435

AN:

25068

East Asian (EAS)

AF:

0.277

AC:

9844

AN:

35532

South Asian (SAS)

AF:

0.141

AC:

11105

AN:

78538

European-Finnish (FIN)

AF:

0.118

AC:

4036

AN:

34082

Middle Eastern (MID)

AF:

0.129

AC:

735

AN:

5682

European-Non Finnish (NFE)

AF:

0.0942

AC:

100901

AN:

1070782

Other (OTH)

AF:

0.120

AC:

6938

AN:

57698

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

5229

10457

15686

20914

26143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3866

7732

11598

15464

19330

<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:

0.109

AC:

16557

AN:

152078

Hom.:

1044

Cov.:

AF XY:

0.114

AC XY:

8450

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.0729

AC:

3025

AN:

41476

American (AMR)

AF:

0.163

AC:

2492

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

591

AN:

3468

East Asian (EAS)

AF:

0.292

AC:

1507

AN:

5154

South Asian (SAS)

AF:

0.157

AC:

756

AN:

4802

European-Finnish (FIN)

AF:

0.120

AC:

1266

AN:

10576

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0970

AC:

6599

AN:

67998

Other (OTH)

AF:

0.117

AC:

246

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

752

1503

2255

3006

3758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.107

Hom.:

1668

Bravo

AF:

0.110

Asia WGS

AF:

0.210

AC:

730

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.45

(source)

DANN

Benign

0.38

PhyloP100

-5.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over