17-69200211-A-G

Position:

• chr17-69200211-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA10	NM_001377321.1	c.1175+1289T>C		intron_variant		ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4	c.1175+1289T>C		intron_variant			NP_525021.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1	c.1175+1289T>C		intron_variant			NM_001377321.1	ENSP00000509702.1
ABCA10	ENST00000522406.5	n.1175+1289T>C		intron_variant		1		ENSP00000429853.1

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

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.732

Alfa AF: 0.738 Hom.: 10341

Bravo AF: 0.758

Asia WGS AF: 0.607 AC: 2111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.43

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: rs7217887; hg19: chr17-67196352;