Genetic Variant ATP10D:c.2434+96C>T (chr4-47558369-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_020453.4(ATP10D):c.2434+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,472,716 control chromosomes in the GnomAD database, including 124,026 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 0.38 ( 11413 hom., cov: 32)

Exomes 𝑓: 0.41 ( 112613 hom. )

Consequence

ATP10D
NM_020453.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.904

Publications

7 publications found

Variant links:

Genes affected

ATP10D (HGNC:13549): (ATPase phospholipid transporting 10D (putative)) Enables glycosylceramide flippase activity. Predicted to be involved in phospholipid translocation. Located in endoplasmic reticulum; nucleoplasm; and plasma membrane. Is integral component of plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ATP10D links:

ENSG00000248254 (HGNC:):

ENSG00000248254 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10D	NM_020453.4 link	c.2434+96C>T		intron_variant	Intron 12 of 22	ENST00000273859.8	NP_065186.3	Q9P241-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ATP10D	ENST00000273859.8 link	c.2434+96C>T	intron_variant	Intron 12 of 22	1	NM_020453.4	ENSP00000273859.3	Q9P241-1
ATP10D	ENST00000503288.6 link	n.*116+96C>T	intron_variant	Intron 5 of 15	2		ENSP00000421536.1	H0Y8M7
ENSG00000248254	ENST00000508081.1 link	n.59-458G>A	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58268

AN:

151972

Hom.:

11405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.337

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.410

AC:

540847

AN:

1320626

Hom.:

112613

AF XY:

0.409

AC XY:

266357

AN XY:

650604

show subpopulations

African (AFR)

AF:

0.294

AC:

8746

AN:

29734

American (AMR)

AF:

0.463

AC:

15248

AN:

32898

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

8972

AN:

20522

East Asian (EAS)

AF:

0.237

AC:

9200

AN:

38782

South Asian (SAS)

AF:

0.379

AC:

26404

AN:

69736

European-Finnish (FIN)

AF:

0.437

AC:

16114

AN:

36866

Middle Eastern (MID)

AF:

0.413

AC:

2105

AN:

5098

European-Non Finnish (NFE)

AF:

0.419

AC:

432258

AN:

1031778

Other (OTH)

AF:

0.395

AC:

21800

AN:

55212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

15597

31194

46790

62387

77984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13336

26672

40008

53344

66680

<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:

0.383

AC:

58317

AN:

152090

Hom.:

11413

Cov.:

AF XY:

0.384

AC XY:

28570

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.306

AC:

12685

AN:

41474

American (AMR)

AF:

0.436

AC:

6659

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.424

AC:

1472

AN:

3470

East Asian (EAS)

AF:

0.207

AC:

1073

AN:

5174

South Asian (SAS)

AF:

0.368

AC:

1772

AN:

4814

European-Finnish (FIN)

AF:

0.455

AC:

4809

AN:

10572

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.421

AC:

28653

AN:

67988

Other (OTH)

AF:

0.370

AC:

779

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1790

3580

5371

7161

8951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.407

Hom.:

53086

Bravo

AF:

0.378

Asia WGS

AF:

0.302

AC:

1052

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.49

(source)

DANN

Benign

0.62

PhyloP100

-0.90

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over