2-215023900-T-G

Variant summary

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

The NM_173076.3(ABCA12):c.1287+1773A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,162 control chromosomes in the GnomAD database, including 46,906 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 0.75 (46906 hom., cov: 32)
• Consequence: ABCA12 NM_173076.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA12	NM_173076.3	c.1287+1773A>C		intron_variant		ENST00000272895.12
LOC124906117	XR_007088073.1	n.1905T>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA12	ENST00000272895.12	c.1287+1773A>C		intron_variant		1	NM_173076.3	P1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113929 AN: 152044 Hom.: 46899 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.749 AC: 113953 AN: 152162 Hom.: 46906 Cov.: 32 AF XY: 0.753 AC XY: 56005 AN XY: 74404

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.765

Alfa AF: 0.831 Hom.: 9749

Bravo AF: 0.716

Asia WGS AF: 0.874 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.2
Dann	Benign	0.77

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: rs952718; hg19: chr2-215888624;