Variant rs1800977 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000435915.1(ENSG00000226334):n.358+259G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,030 control chromosomes in the GnomAD database, including 9,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 9332 hom., cov: 32)

Exomes 𝑓: 0.48 ( 8 hom. )

Consequence

ENST00000435915.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0130

Variant links:

Genes affected

(HGNC:):

links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 9-104928169-G-A is Benign according to our data. Variant chr9-104928169-G-A is described in ClinVar as [Benign]. Clinvar id is 364481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376196	XR_930204.3 linkuse as main transcript	n.1122+259G>A		intron_variant, non_coding_transcript_variant
ABCA1	NM_005502.4 linkuse as main transcript			upstream_gene_variant		ENST00000374736.8	NP_005493.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435915.1 linkuse as main transcript	n.358+259G>A		intron_variant, non_coding_transcript_variant		3
ABCA1	ENST00000374736.8 linkuse as main transcript			upstream_gene_variant		1	NM_005502.4	ENSP00000363868	P1

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

52004

AN:

151846

Hom.:

9328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.351

GnomAD4 exome

AF:

0.485

AC:

AN:

Hom.:

Cov.:

AF XY:

0.560

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.444

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.342

AC:

52035

AN:

151964

Hom.:

9332

Cov.:

AF XY:

0.347

AC XY:

25793

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.443

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.351

Hom.:

19680

Bravo

AF:

0.340

Asia WGS

AF:

0.355

AC:

1229

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 08, 2021	This variant is associated with the following publications: (PMID: 31010439, 11940086, 25527331, 20595220, 14962947, 15935359, 15262183, 17510946) -

Familial High Density Lipoprotein Deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Tangier disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over