rs2888327

chr2-215023290-C-A

Variant summary

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

The NM_173076.3(ABCA12):c.1287+2383G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,244 control chromosomes in the GnomAD database, including 429 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 0.060 (429 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: ABCA12 NM_173076.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

ABCA12 (HGNC:14637): (ATP binding cassette subfamily A member 12) 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, and White). This encoded protein is a member of the ABC1 subfamily, which is the only major ABC subfamily found exclusively in multicellular eukaryotes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

LOC124906117 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA12	NM_173076.3	c.1287+2383G>T		intron_variant		ENST00000272895.12
LOC124906117	XR_007088073.1	n.1295C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA12	ENST00000272895.12	c.1287+2383G>T		intron_variant		1	NM_173076.3	P1

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9137 AN: 152114 Hom.: 427 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.0742

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.0600 AC: 9135 AN: 152232 Hom.: 429 Cov.: 32 AF XY: 0.0595 AC XY: 4428 AN XY: 74420

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0679 Hom.: 69

Bravo AF: 0.0577

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.21
Dann	Benign	0.72

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: rs2888327; hg19: chr2-215888014;