rs2515614

chr9-104922037-A-Cchr9-104922037-A-T

Variant summary

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

The NM_005502.4(ABCA1):c.-93+5898T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,120 control chromosomes in the GnomAD database, including 7,288 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 0.29 (7288 hom., cov: 32)
• Consequence: ABCA1 NM_005502.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.54

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]

LOC124902239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCA1	NM_005502.4	c.-93+5898T>G		intron_variant		ENST00000374736.8
LOC124902239	XR_007061706.1	n.1089-75A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCA1	ENST00000374736.8	c.-93+5898T>G		intron_variant		1	NM_005502.4	P1
ABCA1	ENST00000374733.1	c.-115+5898T>G		intron_variant		2
ABCA1	ENST00000423487.6	c.-93+5898T>G		intron_variant		2
ABCA1	ENST00000678995.1	c.-93+5898T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44252 AN: 152002 Hom.: 7290 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.291 AC: 44261 AN: 152120 Hom.: 7288 Cov.: 32 AF XY: 0.297 AC XY: 22085 AN XY: 74362

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.293

Alfa AF: 0.304 Hom.: 3518

Bravo AF: 0.277

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	11
Dann	Benign	0.69

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: rs2515614; hg19: chr9-107684318;