9-104884939-C-T

Variant names:

• chr9-104884939-C-T
• rs4149268
• NM_005502.4:c.161-371G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005502.4(ABCA1):​c.161-371G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,120 control chromosomes in the GnomAD database, including 17,250 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 0.45 (17250 hom., cov: 33)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 69 publications found

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]

ABCA1 Gene-Disease associations (from GenCC):

• hypoalphalipoproteinemia, primary, 1

  Inheritance: AD Classification: DEFINITIVE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• Tangier disease

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
• apolipoprotein A-I deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005502.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA1	NM_005502.4	MANE Select	c.161-371G>A		intron	N/A	NP_005493.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA1	ENST00000374736.8	TSL:1 MANE Select	c.161-371G>A		intron	N/A	ENSP00000363868.3	O95477
	ABCA1	ENST00000678995.1		c.161-371G>A		intron	N/A	ENSP00000504612.1	A0A7I2V5U0
	ABCA1	ENST00000423487.6	TSL:2	c.161-371G>A		intron	N/A	ENSP00000416623.2	B1AMI2

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68852 AN: 152002 Hom.: 17231 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.453 AC: 68919 AN: 152120 Hom.: 17250 Cov.: 33 AF XY: 0.446 AC XY: 33193 AN XY: 74354

African (AFR) AF: 0.670 AC: 27791 AN: 41500

American (AMR) AF: 0.361 AC: 5506 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1542 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1644 AN: 5166

South Asian (SAS) AF: 0.541 AC: 2609 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10580

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25293 AN: 67990

Other (OTH) AF: 0.453 AC: 955 AN: 2110

Alfa AF: 0.402 Hom.: 57416

Bravo AF: 0.465

Asia WGS AF: 0.479 AC: 1664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.035
DANN	Benign	0.77
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4149268; hg19: chr9-107647220; COSMIC: COSV66058048;