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GeneBe

rs1883025

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215
Variant links:
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]

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ACMG classification

Classification made for transcript

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 UniProt
ABCA1NM_005502.4 linkuse as main transcriptc.66+1594G>A intron_variant ENST00000374736.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCA1ENST00000374736.8 linkuse as main transcriptc.66+1594G>A intron_variant 1 NM_005502.4 P1
ABCA1ENST00000374733.1 linkuse as main transcriptc.-114-12825G>A intron_variant 2
ABCA1ENST00000423487.6 linkuse as main transcriptc.66+1594G>A intron_variant 2
ABCA1ENST00000678995.1 linkuse as main transcriptc.66+1594G>A intron_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

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