Genetic Variant ANKRD13A:c.400+152C>T (chr12-110016585-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_033121.2(ANKRD13A):c.400+152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 670,132 control chromosomes in the GnomAD database, including 2,276 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 0.082 ( 550 hom., cov: 32)

Exomes 𝑓: 0.071 ( 1726 hom. )

Consequence

ANKRD13A
NM_033121.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.176

Publications

5 publications found

Variant links:

Genes affected

ANKRD13A (HGNC:21268): (ankyrin repeat domain 13A) Enables ubiquitin-dependent protein binding activity. Involved in negative regulation of protein localization to endosome and negative regulation of receptor internalization. Located in late endosome; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD13A links:

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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 = 0.0922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033121.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD13A	NM_033121.2	MANE Select	c.400+152C>T		intron	N/A	NP_149112.1	Q8IZ07

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ANKRD13A	ENST00000261739.9	TSL:1 MANE Select	c.400+152C>T	intron	N/A	ENSP00000261739.4	Q8IZ07
ANKRD13A	ENST00000550404.1	TSL:1	n.659+152C>T	intron	N/A
ANKRD13A	ENST00000553025.5	TSL:1	n.136+152C>T	intron	N/A	ENSP00000474172.1	S4R3D2

Frequencies

GnomAD3 genomes

AF:

0.0822

AC:

12490

AN:

151970

Hom.:

549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0946

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0703

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.0831

Gnomad FIN

AF:

0.0713

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0819

Gnomad OTH

AF:

0.100

GnomAD4 exome

AF:

0.0715

AC:

37018

AN:

518044

Hom.:

1726

AF XY:

0.0723

AC XY:

19122

AN XY:

264360

show subpopulations

African (AFR)

AF:

0.0936

AC:

1301

AN:

13896

American (AMR)

AF:

0.0558

AC:

936

AN:

16782

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

1741

AN:

12200

East Asian (EAS)

AF:

0.000232

AC:

AN:

30134

South Asian (SAS)

AF:

0.0717

AC:

2252

AN:

31402

European-Finnish (FIN)

AF:

0.0593

AC:

1685

AN:

28404

Middle Eastern (MID)

AF:

0.120

AC:

228

AN:

1904

European-Non Finnish (NFE)

AF:

0.0751

AC:

26825

AN:

357390

Other (OTH)

AF:

0.0788

AC:

2043

AN:

25932

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1593

3185

4778

6370

7963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.0822

AC:

12500

AN:

152088

Hom.:

550

Cov.:

AF XY:

0.0814

AC XY:

6053

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0946

AC:

3925

AN:

41480

American (AMR)

AF:

0.0702

AC:

1074

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

498

AN:

3470

East Asian (EAS)

AF:

0.000774

AC:

AN:

5168

South Asian (SAS)

AF:

0.0830

AC:

400

AN:

4820

European-Finnish (FIN)

AF:

0.0713

AC:

752

AN:

10540

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0819

AC:

5568

AN:

68002

Other (OTH)

AF:

0.0999

AC:

211

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

577

1154

1732

2309

2886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0843

Hom.:

109

Bravo

AF:

0.0828

Asia WGS

AF:

0.0390

AC:

137

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

2.5

(source)

DANN

Benign

0.76

PhyloP100

-0.18

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