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:

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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=-0.89).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020453.4. 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
	ATP10D	NM_020453.4	MANE Select	c.2434+96C>T		intron	N/A	NP_065186.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ATP10D	ENST00000273859.8	TSL:1 MANE Select	c.2434+96C>T	intron	N/A	ENSP00000273859.3	Q9P241-1
ATP10D	ENST00000917244.1		c.2434+96C>T	intron	N/A	ENSP00000587303.1
ATP10D	ENST00000907879.1		c.2389+96C>T	intron	N/A	ENSP00000577938.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over