Variant 16-2288362-C-G 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_001089.3(ABCA3):c.2701-33G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,534,392 control chromosomes in the GnomAD database, including 423,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38880 hom., cov: 33)

Exomes 𝑓: 0.74 ( 384615 hom. )

Consequence

ABCA3
NM_001089.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.184

Variant links:

Genes affected

ABCA3 (HGNC:33): (ATP binding cassette subfamily A member 3) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. The full transporter encoded by this gene may be involved in development of resistance to xenobiotics and engulfment during programmed cell death. [provided by RefSeq, Jul 2008]

ABCA3 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 (BayesDel_noAF=-0.84).

BP6

Variant 16-2288362-C-G is Benign according to our data. Variant chr16-2288362-C-G is described in ClinVar as [Benign]. Clinvar id is 1185445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA3	NM_001089.3 linkuse as main transcript	c.2701-33G>C		intron_variant		ENST00000301732.10	NP_001080.2	Q99758-1Q4LE27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA3	ENST00000301732.10 linkuse as main transcript	c.2701-33G>C		intron_variant		1	NM_001089.3	ENSP00000301732.5		Q99758-1
ABCA3	ENST00000382381.7 linkuse as main transcript	c.2527-33G>C		intron_variant		1		ENSP00000371818.3		H0Y3H2

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107459

AN:

152034

Hom.:

38852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.791

Gnomad AMR

AF:

0.784

Gnomad ASJ

AF:

0.715

Gnomad EAS

AF:

0.976

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.798

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.728

Gnomad OTH

AF:

0.715

GnomAD3 exomes

AF:

0.789

AC:

110093

AN:

139536

Hom.:

44147

AF XY:

0.792

AC XY:

59305

AN XY:

74872

show subpopulations

Gnomad AFR exome

AF:

0.575

Gnomad AMR exome

AF:

0.857

Gnomad ASJ exome

AF:

0.716

Gnomad EAS exome

AF:

0.975

Gnomad SAS exome

AF:

0.874

Gnomad FIN exome

AF:

0.786

Gnomad NFE exome

AF:

0.733

Gnomad OTH exome

AF:

0.743

GnomAD4 exome

AF:

0.743

AC:

1026806

AN:

1382240

Hom.:

384615

Cov.:

AF XY:

0.747

AC XY:

509046

AN XY:

681676

show subpopulations

Gnomad4 AFR exome

AF:

0.560

Gnomad4 AMR exome

AF:

0.847

Gnomad4 ASJ exome

AF:

0.715

Gnomad4 EAS exome

AF:

0.973

Gnomad4 SAS exome

AF:

0.874

Gnomad4 FIN exome

AF:

0.784

Gnomad4 NFE exome

AF:

0.727

Gnomad4 OTH exome

AF:

0.740

GnomAD4 genome

AF:

0.707

AC:

107530

AN:

152152

Hom.:

38880

Cov.:

AF XY:

0.715

AC XY:

53191

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.563

Gnomad4 AMR

AF:

0.784

Gnomad4 ASJ

AF:

0.715

Gnomad4 EAS

AF:

0.976

Gnomad4 SAS

AF:

0.877

Gnomad4 FIN

AF:

0.798

Gnomad4 NFE

AF:

0.728

Gnomad4 OTH

AF:

0.718

Alfa

AF:

0.682

Hom.:

4557

Bravo

AF:

0.697

Asia WGS

AF:

0.903

AC:

3140

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	GeneDx	Jul 21, 2018	- -

Interstitial lung disease due to ABCA3 deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.23

DANN

Benign

0.38

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