Variant 16-2284553-A-T 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.3704-116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,453,402 control chromosomes in the GnomAD database, including 397,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 38042 hom., cov: 32)

Exomes 𝑓: 0.74 ( 359000 hom. )

Consequence

ABCA3
NM_001089.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.87

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=-0.93).

BP6

Variant 16-2284553-A-T is Benign according to our data. Variant chr16-2284553-A-T is described in ClinVar as [Benign]. Clinvar id is 1270540.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA3	NM_001089.3 linkuse as main transcript	c.3704-116T>A		intron_variant		ENST00000301732.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA3	ENST00000301732.10 linkuse as main transcript	c.3704-116T>A		intron_variant		1	NM_001089.3	P1	Q99758-1
ABCA3	ENST00000382381.7 linkuse as main transcript	c.3530-116T>A		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

106318

AN:

151814

Hom.:

38011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.566

Gnomad AMI

AF:

0.792

Gnomad AMR

AF:

0.782

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.976

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.754

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.720

Gnomad OTH

AF:

0.711

GnomAD4 exome

AF:

0.739

AC:

961531

AN:

1301470

Hom.:

359000

AF XY:

0.743

AC XY:

485208

AN XY:

652998

show subpopulations

Gnomad4 AFR exome

AF:

0.562

Gnomad4 AMR exome

AF:

0.854

Gnomad4 ASJ exome

AF:

0.712

Gnomad4 EAS exome

AF:

0.973

Gnomad4 SAS exome

AF:

0.875

Gnomad4 FIN exome

AF:

0.751

Gnomad4 NFE exome

AF:

0.719

Gnomad4 OTH exome

AF:

0.735

GnomAD4 genome

AF:

0.700

AC:

106392

AN:

151932

Hom.:

38042

Cov.:

AF XY:

0.707

AC XY:

52494

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.566

Gnomad4 AMR

AF:

0.783

Gnomad4 ASJ

AF:

0.712

Gnomad4 EAS

AF:

0.976

Gnomad4 SAS

AF:

0.877

Gnomad4 FIN

AF:

0.754

Gnomad4 NFE

AF:

0.720

Gnomad4 OTH

AF:

0.715

Alfa

AF:

0.700

Hom.:

4466

Bravo

AF:

0.694

Asia WGS

AF:

0.901

AC:

3132

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.82

DANN

Benign

0.68

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