17-69122476-G-A

Position:

• chr17-69122476-G-A

Variant summary

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

The NM_080284.3(ABCA6):​c.1436+763C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,888 control chromosomes in the GnomAD database, including 5,895 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 0.20 (5895 hom., cov: 32)
• Consequence: ABCA6 NM_080284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

Genes affected

ABCA6 (HGNC:36): (ATP binding cassette subfamily A member 6) 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 and may play a role in macrophage lipid homeostasis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA6	NM_080284.3	c.1436+763C>T		intron_variant		ENST00000284425.7	NP_525023.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA6	ENST00000284425.7	c.1436+763C>T		intron_variant		1	NM_080284.3	ENSP00000284425	P1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30051 AN: 151770 Hom.: 5878 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0676

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.198 AC: 30124 AN: 151888 Hom.: 5895 Cov.: 32 AF XY: 0.199 AC XY: 14767 AN XY: 74254

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0676

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.164

Alfa AF: 0.141 Hom.: 577

Bravo AF: 0.223

Asia WGS AF: 0.121 AC: 421 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.20

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: rs8081118; hg19: chr17-67118617;