9-104902020-C-T

Position:

• chr9-104902020-C-T

Variant summary

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

The NM_005502.4(ABCA1):​c.66+1594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,886 control chromosomes in the GnomAD database, including 5,909 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 0.28 (5909 hom., cov: 32)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA1	NM_005502.4	c.66+1594G>A		intron_variant		ENST00000374736.8	NP_005493.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA1	ENST00000374736.8	c.66+1594G>A		intron_variant		1	NM_005502.4	ENSP00000363868	P1
ABCA1	ENST00000374733.1	c.-114-12825G>A		intron_variant		2		ENSP00000363865
ABCA1	ENST00000423487.6	c.66+1594G>A		intron_variant		2		ENSP00000416623
ABCA1	ENST00000678995.1	c.66+1594G>A		intron_variant				ENSP00000504612

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42004 AN: 151770 Hom.: 5896 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.277 AC: 42047 AN: 151886 Hom.: 5909 Cov.: 32 AF XY: 0.273 AC XY: 20297 AN XY: 74274

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.287

Alfa AF: 0.263 Hom.: 10422

Bravo AF: 0.286

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.39

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: rs1883025; hg19: chr9-107664301; COSMIC: COSV66058145;