Variant 17-69223627-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001377321.1(ABCA10):c.35-930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 435,346 control chromosomes in the GnomAD database, including 6,112 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 0.19 ( 3656 hom., cov: 32)

Exomes 𝑓: 0.12 ( 2456 hom. )

Consequence

ABCA10
NM_001377321.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.862

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:

ABCA10 (HGNC:):

ABCA10 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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.35-930G>A		intron_variant		ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4 linkuse as main transcript	c.35-930G>A		intron_variant			NP_525021.3	Q8WWZ4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1 linkuse as main transcript	c.35-930G>A		intron_variant			NM_001377321.1	ENSP00000509702.1		Q8WWZ4-1
ABCA10	ENST00000522406.5 linkuse as main transcript	n.35-930G>A		intron_variant		1		ENSP00000429853.1		Q8WWZ4-5

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29003

AN:

151976

Hom.:

3646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0333

Gnomad SAS

AF:

0.0805

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.181

GnomAD3 exomes

AF:

0.125

AC:

13446

AN:

107788

Hom.:

1089

AF XY:

0.119

AC XY:

7119

AN XY:

59848

show subpopulations

Gnomad AFR exome

AF:

0.352

Gnomad AMR exome

AF:

0.154

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.0329

Gnomad SAS exome

AF:

0.0844

Gnomad FIN exome

AF:

0.136

Gnomad NFE exome

AF:

0.124

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.122

AC:

34510

AN:

283252

Hom.:

2456

Cov.:

AF XY:

0.116

AC XY:

18911

AN XY:

162774

show subpopulations

Gnomad4 AFR exome

AF:

0.337

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.0306

Gnomad4 SAS exome

AF:

0.0855

Gnomad4 FIN exome

AF:

0.134

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.191

AC:

29044

AN:

152094

Hom.:

3656

Cov.:

AF XY:

0.188

AC XY:

13957

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.352

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.0332

Gnomad4 SAS

AF:

0.0797

Gnomad4 FIN

AF:

0.132

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.105

Hom.:

309

Bravo

AF:

0.205

Asia WGS

AF:

0.0860

AC:

299

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.19

DANN

Benign

0.48

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