chr17-69179527-C-T

Variant names:

• chr17-69179527-C-T
• rs1024598
• NM_001377321.1:c.2769+2626G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.86).
• 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 rank	MANE	Protein	UniProt
ABCA10	NM_001377321.1	c.2769+2626G>A		intron_variant	Intron 22 of 38	ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4	c.2769+2626G>A		intron_variant	Intron 23 of 39		NP_525021.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1	c.2769+2626G>A		intron_variant	Intron 22 of 38		NM_001377321.1	ENSP00000509702.1
ABCA10	ENST00000522406.5	n.*1609-519G>A		intron_variant	Intron 23 of 40	1		ENSP00000429853.1

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

African (AFR) AF: 0.353 AC: 14635 AN: 41466

American (AMR) AF: 0.562 AC: 8579 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1871 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1741 AN: 5142

South Asian (SAS) AF: 0.614 AC: 2958 AN: 4814

European-Finnish (FIN) AF: 0.642 AC: 6790 AN: 10576

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45540 AN: 67934

Other (OTH) AF: 0.561 AC: 1186 AN: 2114

Alfa AF: 0.604 Hom.: 5062

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
PhyloP100		0.43
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: rs1024598; hg19: chr17-67175668;