Variant chr17-69153832-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001377321.1(ABCA10):c.3964C>T(p.Arg1322Ter) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 1,611,562 control chromosomes in the GnomAD database, including 3,739 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.073 ( 537 hom., cov: 32)

Exomes 𝑓: 0.060 ( 3202 hom. )

Consequence

ABCA10
NM_001377321.1 stop_gained, splice_region

Scores

Splicing: ADA: 0.004318

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Variant links:

Genes affected

ABCA10 (HGNC:30): (ATP binding cassette subfamily A member 10) 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, but neither the substrate nor the function of this gene is known. [provided by RefSeq, Jul 2008]

ABCA10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA10	NM_001377321.1 linkuse as main transcript	c.3964C>T	p.Arg1322Ter	stop_gained, splice_region_variant	32/39	ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4 linkuse as main transcript	c.3964C>T	p.Arg1322Ter	stop_gained, splice_region_variant	33/40		NP_525021.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1 linkuse as main transcript	c.3964C>T	p.Arg1322Ter	stop_gained, splice_region_variant	32/39		NM_001377321.1	ENSP00000509702	P1	Q8WWZ4-1

Frequencies

GnomAD3 genomes

AF:

0.0729

AC:

11075

AN:

151950

Hom.:

537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0711

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.0647

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.0696

Gnomad FIN

AF:

0.0790

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0523

Gnomad OTH

AF:

0.0800

GnomAD3 exomes

AF:

0.0811

AC:

20208

AN:

249050

Hom.:

1084

AF XY:

0.0760

AC XY:

10226

AN XY:

134520

show subpopulations

Gnomad AFR exome

AF:

0.0743

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.0653

Gnomad EAS exome

AF:

0.139

Gnomad SAS exome

AF:

0.0682

Gnomad FIN exome

AF:

0.0870

Gnomad NFE exome

AF:

0.0507

Gnomad OTH exome

AF:

0.0760

GnomAD4 exome

AF:

0.0602

AC:

87900

AN:

1459494

Hom.:

3202

Cov.:

AF XY:

0.0597

AC XY:

43357

AN XY:

725910

show subpopulations

Gnomad4 AFR exome

AF:

0.0736

Gnomad4 AMR exome

AF:

0.166

Gnomad4 ASJ exome

AF:

0.0629

Gnomad4 EAS exome

AF:

0.118

Gnomad4 SAS exome

AF:

0.0697

Gnomad4 FIN exome

AF:

0.0851

Gnomad4 NFE exome

AF:

0.0512

Gnomad4 OTH exome

AF:

0.0664

GnomAD4 genome

AF:

0.0730

AC:

11095

AN:

152068

Hom.:

537

Cov.:

AF XY:

0.0768

AC XY:

5708

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.0711

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.0647

Gnomad4 EAS

AF:

0.121

Gnomad4 SAS

AF:

0.0690

Gnomad4 FIN

AF:

0.0790

Gnomad4 NFE

AF:

0.0524

Gnomad4 OTH

AF:

0.0825

Alfa

AF:

0.0586

Hom.:

1022

Bravo

AF:

0.0789

TwinsUK

AF:

0.0537

AC:

199

ALSPAC

AF:

0.0485

AC:

187

ESP6500AA

AF:

0.0738

AC:

325

ESP6500EA

AF:

0.0530

AC:

456

ExAC

AF:

0.0747

AC:

9064

Asia WGS

AF:

0.0910

AC:

318

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Uncertain

-0.030

CADD

Pathogenic

DANN

Benign

0.87

Eigen

Benign

-0.88

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0092

MutationTaster

Benign

1.0e-37

P;P

Vest4

0.031

GERP RS

-7.5

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0043

dbscSNV1_RF

Benign

0.48

SpliceAI score (max)

0.030

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