16-2314050-C-G

Position:

• chr16-2314050-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001089.3(ABCA3):​c.1111+3233G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,966 control chromosomes in the GnomAD database, including 6,712 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6712 hom., cov: 31)
• Consequence: ABCA3 NM_001089.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA3	NM_001089.3	c.1111+3233G>C		intron_variant		ENST00000301732.10	NP_001080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA3	ENST00000301732.10	c.1111+3233G>C		intron_variant		1	NM_001089.3	ENSP00000301732.5
ABCA3	ENST00000382381.7	c.1111+3233G>C		intron_variant		1		ENSP00000371818.3
ABCA3	ENST00000563623.5	n.1674+3233G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44332 AN: 151848 Hom.: 6696 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.292 AC: 44380 AN: 151966 Hom.: 6712 Cov.: 31 AF XY: 0.297 AC XY: 22050 AN XY: 74258

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.302

Alfa AF: 0.285 Hom.: 806

Bravo AF: 0.303

Asia WGS AF: 0.297 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.14

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: rs323069; hg19: chr16-2364051;