Variant 4-47523071-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020453.4(ATP10D):c.545G>A(p.Arg182His) variant causes a missense change. The variant allele was found at a frequency of 0.00321 in 1,613,006 control chromosomes in the GnomAD database, including 146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 70 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 76 hom. )

Consequence

ATP10D
NM_020453.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.83

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032405555).

BP6

Variant 4-47523071-G-A is Benign according to our data. Variant chr4-47523071-G-A is described in ClinVar as [Benign]. Clinvar id is 791977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10D	NM_020453.4 link	c.545G>A	p.Arg182His	missense_variant	4/23	ENST00000273859.8	NP_065186.3	Q9P241-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10D	ENST00000273859.8 link	c.545G>A	p.Arg182His	missense_variant	4/23	1	NM_020453.4	ENSP00000273859.3		Q9P241-1
ATP10D	ENST00000504445.1 link	c.545G>A	p.Arg182His	missense_variant	4/10	1		ENSP00000420909.1		Q6PEW3

Frequencies

GnomAD3 genomes

AF:

0.0178

AC:

2686

AN:

151122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0620

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00614

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000280

Gnomad OTH

AF:

0.0125

GnomAD3 exomes

AF:

0.00482

AC:

1210

AN:

251256

Hom.:

AF XY:

0.00354

AC XY:

480

AN XY:

135778

show subpopulations

Gnomad AFR exome

AF:

0.0646

Gnomad AMR exome

AF:

0.00396

Gnomad ASJ exome

AF:

0.0000993

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000114

Gnomad OTH exome

AF:

0.00131

GnomAD4 exome

AF:

0.00171

AC:

2497

AN:

1461766

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

1061

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.0597

Gnomad4 AMR exome

AF:

0.00407

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000580

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000944

Gnomad4 OTH exome

AF:

0.00318

GnomAD4 genome

AF:

0.0178

AC:

2687

AN:

151240

Hom.:

Cov.:

AF XY:

0.0177

AC XY:

1309

AN XY:

73792

show subpopulations

Gnomad4 AFR

AF:

0.0618

Gnomad4 AMR

AF:

0.00613

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000280

Gnomad4 OTH

AF:

0.0124

Alfa

AF:

0.00287

Hom.:

Bravo

AF:

0.0196

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0604

AC:

266

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00585

AC:

710

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000296

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 17, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.18

CADD

Uncertain

DANN

Benign

0.89

DEOGEN2

Benign

0.24

T;.

Eigen

Benign

-0.039

Eigen_PC

Benign

0.12

FATHMM_MKL

Uncertain

0.92

LIST_S2

Uncertain

0.90

D;D

MetaRNN

Benign

0.0032

T;T

MetaSVM

Benign

-0.33

MutationAssessor

Uncertain

2.2

M;.

PrimateAI

Benign

0.28

PROVEAN

Benign

-1.9

N;D

REVEL

Uncertain

0.30

Sift

Benign

0.22

T;T

Sift4G

Benign

0.57

T;T

Polyphen

0.016

B;B

Vest4

0.25

MVP

0.87

MPC

0.19

ClinPred

0.032

GERP RS

5.1

Varity_R

0.14

gMVP

0.57

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over