rs2014467

chr16-2286393-T-Cchr16-2286393-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001089.3(ABCA3):c.3278+301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,102 control chromosomes in the GnomAD database, including 6,958 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (6958 hom., cov: 32)
• Consequence: ABCA3 NM_001089.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.37

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 16-2286393-T-C is Benign according to our data. Variant chr16-2286393-T-C is described in ClinVar as [Benign]. Clinvar id is 1262016.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA3	NM_001089.3	c.3278+301A>G		intron_variant		ENST00000301732.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA3	ENST00000301732.10	c.3278+301A>G		intron_variant		1	NM_001089.3	P1
ABCA3	ENST00000382381.7	c.3104+301A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40773 AN: 151984 Hom.: 6945 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.296

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.268 AC: 40799 AN: 152102 Hom.: 6958 Cov.: 32 AF XY: 0.276 AC XY: 20555 AN XY: 74358

Gnomad4 AFR AF: 0.0640

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.296

Alfa AF: 0.311 Hom.: 3906

Bravo AF: 0.263

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.052
Dann	Benign	0.36

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

Other links and lift over

dbSNP: rs2014467; hg19: chr16-2336394;