rs2575875

Variant names:

• chr9-104900213-G-A
• rs2575875
• NM_005502.4:c.66+3401C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005502.4(ABCA1):​c.66+3401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,952 control chromosomes in the GnomAD database, including 17,147 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.45 (17147 hom., cov: 31)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.108
• Publications: 24 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: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• apolipoprotein A-I deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 9-104900213-G-A is Benign according to our data. Variant chr9-104900213-G-A is described in ClinVar as Benign. ClinVar VariationId is 1262580.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA1	NM_005502.4	c.66+3401C>T		intron_variant	Intron 2 of 49	ENST00000374736.8	NP_005493.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA1	ENST00000374736.8	c.66+3401C>T		intron_variant	Intron 2 of 49	1	NM_005502.4	ENSP00000363868.3
ABCA1	ENST00000678995.1	c.66+3401C>T		intron_variant	Intron 2 of 49			ENSP00000504612.1
ABCA1	ENST00000423487.6	c.66+3401C>T		intron_variant	Intron 2 of 7	2		ENSP00000416623.2
ABCA1	ENST00000374733.1	c.-114-11018C>T		intron_variant	Intron 1 of 4	2		ENSP00000363865.1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69024 AN: 151832 Hom.: 17096 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.455 AC: 69132 AN: 151952 Hom.: 17147 Cov.: 31 AF XY: 0.449 AC XY: 33341 AN XY: 74240

African (AFR) AF: 0.661 AC: 27374 AN: 41432

American (AMR) AF: 0.394 AC: 6017 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5160

South Asian (SAS) AF: 0.523 AC: 2516 AN: 4808

European-Finnish (FIN) AF: 0.283 AC: 2984 AN: 10554

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25462 AN: 67942

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.409 Hom.: 22440

Bravo AF: 0.470

Asia WGS AF: 0.460 AC: 1597 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 16, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 31039173) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		-0.11
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: rs2575875; hg19: chr9-107662494; COSMIC: COSV66058124;