chr16-2295663-C-A

Position:

• chr16-2295663-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001089.3(ABCA3):​c.2341G>T​(p.Val781Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ABCA3 NM_001089.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3551172).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA3	NM_001089.3	c.2341G>T	p.Val781Leu	missense_variant	18/33	ENST00000301732.10	NP_001080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA3	ENST00000301732.10	c.2341G>T	p.Val781Leu	missense_variant	18/33	1	NM_001089.3	ENSP00000301732	P1
ABCA3	ENST00000382381.7	c.2167G>T	p.Val723Leu	missense_variant	17/32	1		ENSP00000371818
ABCA3	ENST00000563623.5	n.2904G>T		non_coding_transcript_exon_variant	18/20	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Benign	-0.014	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	14
DANN	Benign	0.95
DEOGEN2	Benign	0.28	T;.
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.88
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.83	T;D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.36	T;T
MetaSVM	Benign	-0.29	T
MutationAssessor	Benign	1.1	L;.
MutationTaster	Benign	0.99	N;N
PrimateAI	Benign	0.32	T
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.26
Sift	Uncertain	0.016	D;D
Sift4G	Uncertain	0.018	D;D
Polyphen		0.10	B;.
Vest4		0.52
MutPred		0.33		Gain of catalytic residue at V781 (P = 0.0796);.;
MVP		0.49
MPC		0.29
ClinPred		0.23	T
GERP RS		-4.6
Varity_R		0.11
gMVP		0.74

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: rs771821923; hg19: chr16-2345664;