Variant chr19-1047688-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_019112.4(ABCA7):c.2269+34C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 1,545,166 control chromosomes in the GnomAD database, including 8,985 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 0.076 ( 732 hom., cov: 33)

Exomes 𝑓: 0.095 ( 8253 hom. )

Consequence

ABCA7
NM_019112.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.634

Variant links:

Genes affected

ABCA7 (HGNC:37): (ATP binding cassette subfamily A member 7) The 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 intra-cellular 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. This full transporter has been detected predominantly in myelo-lymphatic tissues with the highest expression in peripheral leukocytes, thymus, spleen, and bone marrow. The function of this protein is not yet known; however, the expression pattern suggests a role in lipid homeostasis in cells of the immune system. [provided by RefSeq, Jul 2008]

ABCA7 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA7	NM_019112.4 link	c.2269+34C>G		intron_variant		ENST00000263094.11	NP_061985.2	Q8IZY2-1B3KUJ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA7	ENST00000263094.11 link	c.2269+34C>G		intron_variant		5	NM_019112.4	ENSP00000263094.6		Q8IZY2-1
ABCA7	ENST00000433129.6 link	n.2949+34C>G		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0760

AC:

11544

AN:

151844

Hom.:

724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.0708

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0313

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0894

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.104

AC:

17104

AN:

164352

Hom.:

1374

AF XY:

0.105

AC XY:

9674

AN XY:

91800

show subpopulations

Gnomad AFR exome

AF:

0.0149

Gnomad AMR exome

AF:

0.0494

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.343

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.0337

Gnomad NFE exome

AF:

0.0909

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0952

AC:

132641

AN:

1393206

Hom.:

8253

Cov.:

AF XY:

0.0959

AC XY:

65853

AN XY:

686682

show subpopulations

Gnomad4 AFR exome

AF:

0.0154

Gnomad4 AMR exome

AF:

0.0514

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.366

Gnomad4 SAS exome

AF:

0.114

Gnomad4 FIN exome

AF:

0.0356

Gnomad4 NFE exome

AF:

0.0889

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0761

AC:

11559

AN:

151960

Hom.:

732

Cov.:

AF XY:

0.0750

AC XY:

5566

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.0203

Gnomad4 AMR

AF:

0.0707

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.0313

Gnomad4 NFE

AF:

0.0893

Gnomad4 OTH

AF:

0.114

Alfa

AF:

0.0490

Hom.:

Bravo

AF:

0.0761

Asia WGS

AF:

0.223

AC:

774

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.0

DANN

Benign

0.67

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over