rs1024598

Positions:

• chr17-69179527-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001377321.1(ABCA10):​c.2769+2626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,994 control chromosomes in the GnomAD database, including 25,006 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 0.55 (25006 hom., cov: 31)
• Consequence: ABCA10 NM_001377321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA10	NM_001377321.1	c.2769+2626G>A		intron_variant		ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4	c.2769+2626G>A		intron_variant			NP_525021.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1	c.2769+2626G>A		intron_variant			NM_001377321.1	ENSP00000509702	P1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84189 AN: 151876 Hom.: 25012 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.554 AC: 84194 AN: 151994 Hom.: 25006 Cov.: 31 AF XY: 0.551 AC XY: 40953 AN XY: 74284

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.561

Alfa AF: 0.611 Hom.: 5020

Bravo AF: 0.535

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs1024598; hg19: chr17-67175668;