17-69200211-A-G

Variant names:

• chr17-69200211-A-G
• rs7217887
• NM_001377321.1:c.1175+1289T>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.1175+1289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,104 control chromosomes in the GnomAD database, including 43,703 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 0.75 (43703 hom., cov: 32)
• Consequence: ABCA10 NM_001377321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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.1175+1289T>C		intron	N/A	NP_001364250.1
	ABCA10	NM_080282.4		c.1175+1289T>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.1175+1289T>C		intron	N/A	ENSP00000509702.1
	ABCA10	ENST00000269081.8	TSL:1	c.1175+1289T>C		intron	N/A	ENSP00000269081.4
	ABCA10	ENST00000518929.5	TSL:1	n.1007-3089T>C		intron	N/A	ENSP00000430341.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114375 AN: 151986 Hom.: 43661 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.753 AC: 114476 AN: 152104 Hom.: 43703 Cov.: 32 AF XY: 0.751 AC XY: 55833 AN XY: 74362

African (AFR) AF: 0.860 AC: 35709 AN: 41532

American (AMR) AF: 0.764 AC: 11666 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3466

East Asian (EAS) AF: 0.460 AC: 2377 AN: 5168

South Asian (SAS) AF: 0.687 AC: 3308 AN: 4814

European-Finnish (FIN) AF: 0.721 AC: 7624 AN: 10578

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49191 AN: 67952

Other (OTH) AF: 0.732 AC: 1546 AN: 2112

Alfa AF: 0.741 Hom.: 10623

Bravo AF: 0.758

Asia WGS AF: 0.607 AC: 2111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.43
PhyloP100		-0.080
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: rs7217887; hg19: chr17-67196352;