Genetic Variant NM_001370597.1:c.360T>C (chr1-154331500-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_001370597.1(ATP8B2):c.360T>C(p.Asn120Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,613,738 control chromosomes in the GnomAD database, including 76,216 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 ( 6941 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69275 hom. )

Consequence

ATP8B2
NM_001370597.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334

Publications

23 publications found

Variant links:

Genes affected

ATP8B2 (HGNC:13534): (ATPase phospholipid transporting 8B2) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ATP8B2 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP7

Synonymous conserved (PhyloP=0.334 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B2	NM_001370597.1 link	c.360T>C	p.Asn120Asn	synonymous_variant	Exon 6 of 28	ENST00000368489.6	NP_001357526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B2	ENST00000368489.6 link	c.360T>C	p.Asn120Asn	synonymous_variant	Exon 6 of 28	1	NM_001370597.1	ENSP00000357475.4		A0A5K1VW70

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45737

AN:

151958

Hom.:

6931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.287

GnomAD2 exomes

AF:

0.292

AC:

73402

AN:

251466

AF XY:

0.299

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.367

Gnomad NFE exome

AF:

0.303

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.305

AC:

446234

AN:

1461662

Hom.:

69275

Cov.:

AF XY:

0.307

AC XY:

223351

AN XY:

727136

show subpopulations

African (AFR)

AF:

0.317

AC:

10601

AN:

33470

American (AMR)

AF:

0.216

AC:

9661

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

5551

AN:

26136

East Asian (EAS)

AF:

0.227

AC:

9029

AN:

39698

South Asian (SAS)

AF:

0.345

AC:

29720

AN:

86252

European-Finnish (FIN)

AF:

0.361

AC:

19303

AN:

53418

Middle Eastern (MID)

AF:

0.261

AC:

1500

AN:

5750

European-Non Finnish (NFE)

AF:

0.308

AC:

342725

AN:

1111830

Other (OTH)

AF:

0.300

AC:

18144

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

17921

35842

53764

71685

89606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11208

22416

33624

44832

56040

<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:

0.301

AC:

45780

AN:

152076

Hom.:

6941

Cov.:

AF XY:

0.304

AC XY:

22569

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.311

AC:

12895

AN:

41462

American (AMR)

AF:

0.246

AC:

3768

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

708

AN:

3466

East Asian (EAS)

AF:

0.222

AC:

1149

AN:

5170

South Asian (SAS)

AF:

0.324

AC:

1559

AN:

4814

European-Finnish (FIN)

AF:

0.374

AC:

3955

AN:

10588

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.305

AC:

20721

AN:

67972

Other (OTH)

AF:

0.292

AC:

617

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1663

3326

4988

6651

8314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.299

Hom.:

31338

Bravo

AF:

0.289

Asia WGS

AF:

0.271

AC:

940

AN:

3478

EpiCase

AF:

0.299

EpiControl

AF:

0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=99/1

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