Variant 16-2299370-T-C 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.1741+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,611,130 control chromosomes in the GnomAD database, including 207,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 16323 hom., cov: 32)

Exomes 𝑓: 0.51 ( 191290 hom. )

Consequence

ABCA3
NM_001089.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.54

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 16-2299370-T-C is Benign according to our data. Variant chr16-2299370-T-C is described in ClinVar as [Benign]. Clinvar id is 1185446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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.1741+33A>G		intron_variant		ENST00000301732.10	NP_001080.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
ABCA3	ENST00000301732.10 linkuse as main transcript	c.1741+33A>G	intron_variant	1	NM_001089.3	ENSP00000301732	P1	Q99758-1
ABCA3	ENST00000382381.7 linkuse as main transcript	c.1567+33A>G	intron_variant	1		ENSP00000371818
ABCA3	ENST00000563623.5 linkuse as main transcript	n.2304+33A>G	intron_variant, non_coding_transcript_variant	1

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

68394

AN:

151846

Hom.:

16298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.481

GnomAD3 exomes

AF:

0.507

AC:

126243

AN:

248760

Hom.:

32844

AF XY:

0.504

AC XY:

67941

AN XY:

134772

show subpopulations

Gnomad AFR exome

AF:

0.280

Gnomad AMR exome

AF:

0.589

Gnomad ASJ exome

AF:

0.457

Gnomad EAS exome

AF:

0.551

Gnomad SAS exome

AF:

0.459

Gnomad FIN exome

AF:

0.555

Gnomad NFE exome

AF:

0.517

Gnomad OTH exome

AF:

0.507

GnomAD4 exome

AF:

0.509

AC:

743207

AN:

1459166

Hom.:

191290

Cov.:

AF XY:

0.507

AC XY:

368089

AN XY:

726056

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.583

Gnomad4 ASJ exome

AF:

0.461

Gnomad4 EAS exome

AF:

0.554

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.557

Gnomad4 NFE exome

AF:

0.517

Gnomad4 OTH exome

AF:

0.489

GnomAD4 genome

AF:

0.450

AC:

68456

AN:

151964

Hom.:

16323

Cov.:

AF XY:

0.455

AC XY:

33839

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.536

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.543

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.564

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.479

Alfa

AF:

0.467

Hom.:

3296

Bravo

AF:

0.446

Asia WGS

AF:

0.457

AC:

1588

AN:

3474

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	Jun 29, 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

-0.91

CADD

Benign

0.27

DANN

Benign

0.18

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