rs12938039

Variant names:

• chr17-69224495-C-G
• rs12938039
• NM_001377321.1:c.34+830G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001377321.1(ABCA10):​c.34+830G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,872 control chromosomes in the GnomAD database, including 12,547 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 0.37 (12547 hom., cov: 30)
• Consequence: ABCA10 NM_001377321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA10	NM_001377321.1	MANE Select	c.34+830G>C		intron	N/A	NP_001364250.1
	ABCA10	NM_080282.4		c.34+830G>C		intron	N/A	NP_525021.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA10	ENST00000690296.1	MANE Select	c.34+830G>C		intron	N/A	ENSP00000509702.1
	ABCA10	ENST00000269081.8	TSL:1	c.34+830G>C		intron	N/A	ENSP00000269081.4
	ABCA10	ENST00000518929.5	TSL:1	n.34+830G>C		intron	N/A	ENSP00000430341.1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56475 AN: 151754 Hom.: 12548 Cov.: 30

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.411

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.372 AC: 56465 AN: 151872 Hom.: 12547 Cov.: 30 AF XY: 0.373 AC XY: 27691 AN XY: 74196

African (AFR) AF: 0.119 AC: 4926 AN: 41468

American (AMR) AF: 0.368 AC: 5613 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1960 AN: 5170

South Asian (SAS) AF: 0.515 AC: 2475 AN: 4806

European-Finnish (FIN) AF: 0.456 AC: 4781 AN: 10492

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33630 AN: 67908

Other (OTH) AF: 0.411 AC: 868 AN: 2112

Alfa AF: 0.429 Hom.: 1959

Bravo AF: 0.349

Asia WGS AF: 0.436 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.084
DANN	Benign	0.42
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12938039; hg19: chr17-67220636;