9-104866823-T-C

Position:

• chr9-104866823-T-C

Variant summary

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

The NM_005502.4(ABCA1):​c.422-5023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,960 control chromosomes in the GnomAD database, including 22,515 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 0.51 (22515 hom., cov: 31)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA1	NM_005502.4	c.422-5023A>G		intron_variant		ENST00000374736.8	NP_005493.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA1	ENST00000374736.8	c.422-5023A>G		intron_variant		1	NM_005502.4	ENSP00000363868	P1
ABCA1	ENST00000374733.1	c.242-5023A>G		intron_variant		2		ENSP00000363865
ABCA1	ENST00000423487.6	c.422-5023A>G		intron_variant		2		ENSP00000416623
ABCA1	ENST00000678995.1	c.422-5023A>G		intron_variant				ENSP00000504612

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77517 AN: 151842 Hom.: 22462 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.511 AC: 77625 AN: 151960 Hom.: 22515 Cov.: 31 AF XY: 0.502 AC XY: 37264 AN XY: 74260

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.534

Alfa AF: 0.430 Hom.: 19321

Bravo AF: 0.528

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.40

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: rs4743764; hg19: chr9-107629104;