rs2472507

Positions:

• chr9-104924912-A-C
• chr9-104924912-A-G

Variant summary

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

The NM_005502.4(ABCA1):​c.-93+3023T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,194 control chromosomes in the GnomAD database, including 3,121 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 0.19 (3121 hom., cov: 33)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757

Genes affected

ABCA1 (HGNC:29): (ATP binding cassette subfamily A member 1) 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. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in both alleles of this gene cause Tangier disease and familial high-density lipoprotein (HDL) deficiency. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA1	NM_005502.4	c.-93+3023T>G		intron_variant		ENST00000374736.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA1	ENST00000374736.8	c.-93+3023T>G		intron_variant		1	NM_005502.4	P1
ABCA1	ENST00000374733.1	c.-115+3023T>G		intron_variant		2
ABCA1	ENST00000423487.6	c.-93+3023T>G		intron_variant		2
ABCA1	ENST00000678995.1	c.-93+3023T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28709 AN: 152076 Hom.: 3128 Cov.: 33

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.189 AC: 28709 AN: 152194 Hom.: 3121 Cov.: 33 AF XY: 0.194 AC XY: 14459 AN XY: 74396

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.197

Alfa AF: 0.188 Hom.: 392

Bravo AF: 0.176

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.66

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: rs2472507; hg19: chr9-107687193;