Variant 5-82312744-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_169870.1(ATP6AP1L):n.2235T>C variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,590,108 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0056 ( 35 hom. )

Consequence

ATP6AP1L
NR_169870.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.77

Variant links:

Genes affected

ATP6AP1L (HGNC:):

ATP6AP1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.02450344).

BP6

Variant 5-82312744-T-C is Benign according to our data. Variant chr5-82312744-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2655574.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
ATP6AP1L	NR_169870.1 linkuse as main transcript	n.2235T>C	non_coding_transcript_exon_variant	11/12
ATP6AP1L	NR_172106.1 linkuse as main transcript	n.1829T>C	non_coding_transcript_exon_variant	9/10
ATP6AP1L	NR_172107.1 linkuse as main transcript	n.2329T>C	non_coding_transcript_exon_variant	10/11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ATP6AP1L	ENST00000380167.8 linkuse as main transcript	n.1590T>C	non_coding_transcript_exon_variant	9/10	2
ATP6AP1L	ENST00000508366.5 linkuse as main transcript	n.1483T>C	non_coding_transcript_exon_variant	2/8	2
ATP6AP1L	ENST00000514672.1 linkuse as main transcript	n.306T>C	non_coding_transcript_exon_variant	2/3	2
ATP6AP1L	ENST00000643922.1 linkuse as main transcript	n.617T>C	non_coding_transcript_exon_variant	6/7

Frequencies

GnomAD3 genomes

AF:

0.00418

AC:

636

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00570

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00660

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00382

AC:

870

AN:

227500

Hom.:

AF XY:

0.00370

AC XY:

458

AN XY:

123708

show subpopulations

Gnomad AFR exome

AF:

0.00169

Gnomad AMR exome

AF:

0.00478

Gnomad ASJ exome

AF:

0.000215

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000113

Gnomad FIN exome

AF:

0.00388

Gnomad NFE exome

AF:

0.00553

Gnomad OTH exome

AF:

0.00681

GnomAD4 exome

AF:

0.00559

AC:

8032

AN:

1437782

Hom.:

Cov.:

AF XY:

0.00534

AC XY:

3817

AN XY:

714622

show subpopulations

Gnomad4 AFR exome

AF:

0.000914

Gnomad4 AMR exome

AF:

0.00478

Gnomad4 ASJ exome

AF:

0.000118

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000135

Gnomad4 FIN exome

AF:

0.00437

Gnomad4 NFE exome

AF:

0.00660

Gnomad4 OTH exome

AF:

0.00472

GnomAD4 genome

AF:

0.00418

AC:

637

AN:

152326

Hom.:

Cov.:

AF XY:

0.00389

AC XY:

290

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00569

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00320

Gnomad4 NFE

AF:

0.00661

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00537

Hom.:

Bravo

AF:

0.00429

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00535

AC:

ExAC

AF:

0.00383

AC:

465

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

ATP6AP1L: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.45

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Uncertain

0.050

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.34

Eigen

Pathogenic

0.78

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.81

M_CAP

Benign

0.019

MetaRNN

Benign

0.025

MetaSVM

Uncertain

-0.10

MutationAssessor

Uncertain

2.6

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.46

PROVEAN

Pathogenic

-4.5

REVEL

Pathogenic

0.65

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.65

MVP

0.21

ClinPred

0.022

GERP RS

5.7

Varity_R

0.90

gMVP

0.83

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