chr2-215053065-A-G

Position:

• chr2-215053065-A-G

Variant summary

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

The ENST00000272895.12(ABCA12):​c.410-481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,930 control chromosomes in the GnomAD database, including 3,397 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 0.21 (3397 hom., cov: 32)
• Consequence: ABCA12 ENST00000272895.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

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]

ENSG00000227769 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA12	NM_173076.3	c.410-481T>C		intron_variant		ENST00000272895.12	NP_775099.2
ABCA12	XM_011510951.3	c.410-481T>C		intron_variant			XP_011509253.1
ABCA12	NR_103740.2	n.828-481T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA12	ENST00000272895.12	c.410-481T>C		intron_variant		1	NM_173076.3	ENSP00000272895.7
ENSG00000227769	ENST00000626134.2	n.404+8548A>G		intron_variant		5
ENSG00000227769	ENST00000626771.1	n.338+8548A>G		intron_variant		5
ENSG00000227769	ENST00000628464.2	n.1021+8548A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31204 AN: 151812 Hom.: 3402 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.205 AC: 31212 AN: 151930 Hom.: 3397 Cov.: 32 AF XY: 0.203 AC XY: 15038 AN XY: 74210

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.214

Alfa AF: 0.207 Hom.: 5907

Bravo AF: 0.214

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	13
DANN	Benign	0.64

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: rs17430358; hg19: chr2-215917789;