Variant chr17-69086646-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_080284.3(ABCA6):c.3909A>G(p.Ala1303=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00647 in 1,612,284 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 3 hom., cov: 30)

Exomes 𝑓: 0.0066 ( 67 hom. )

Consequence

ABCA6
NM_080284.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

ABCA6 (HGNC:36): (ATP binding cassette subfamily A member 6) 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, and White). This encoded 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 gene is clustered among 4 other ABC1 family members on 17q24 and may play a role in macrophage lipid homeostasis. [provided by RefSeq, Jul 2008]

ABCA6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 17-69086646-T-C is Benign according to our data. Variant chr17-69086646-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2648162.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA6	NM_080284.3 linkuse as main transcript	c.3909A>G	p.Ala1303=	synonymous_variant	30/39	ENST00000284425.7	NP_525023.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA6	ENST00000284425.7 linkuse as main transcript	c.3909A>G	p.Ala1303=	synonymous_variant	30/39	1	NM_080284.3	ENSP00000284425	P1	Q8N139-1
ABCA6	ENST00000446604.6 linkuse as main transcript	n.1175A>G		non_coding_transcript_exon_variant	9/18	2
ABCA6	ENST00000589482.1 linkuse as main transcript	n.356A>G		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.00538

AC:

819

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00196

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00932

Gnomad FIN

AF:

0.0199

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00693

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00608

AC:

1528

AN:

251164

Hom.:

AF XY:

0.00662

AC XY:

899

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.000985

Gnomad AMR exome

AF:

0.00208

Gnomad ASJ exome

AF:

0.000993

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00882

Gnomad FIN exome

AF:

0.0174

Gnomad NFE exome

AF:

0.00659

Gnomad OTH exome

AF:

0.00588

GnomAD4 exome

AF:

0.00658

AC:

9613

AN:

1460064

Hom.:

Cov.:

AF XY:

0.00684

AC XY:

4970

AN XY:

726488

show subpopulations

Gnomad4 AFR exome

AF:

0.000987

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.000805

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.0168

Gnomad4 NFE exome

AF:

0.00662

Gnomad4 OTH exome

AF:

0.00509

GnomAD4 genome

AF:

0.00538

AC:

819

AN:

152220

Hom.:

Cov.:

AF XY:

0.00619

AC XY:

461

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00116

Gnomad4 AMR

AF:

0.00196

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00933

Gnomad4 FIN

AF:

0.0199

Gnomad4 NFE

AF:

0.00693

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00574

Hom.:

Bravo

AF:

0.00335

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00578

EpiControl

AF:

0.00498

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

ABCA6: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.9

DANN

Benign

0.61

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over