17-69223627-C-T

Variant names:

• chr17-69223627-C-T
• rs1468512
• NM_001377321.1:c.35-930G>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.35-930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 435,346 control chromosomes in the GnomAD database, including 6,112 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 0.19 (3656 hom., cov: 32)
  • Exomes 𝑓: 0.12 (2456 hom.)
• Consequence: ABCA10 NM_001377321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA10	NM_001377321.1	MANE Select	c.35-930G>A		intron	N/A	NP_001364250.1	Q8WWZ4-1
	ABCA10	NM_080282.4		c.35-930G>A		intron	N/A	NP_525021.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCA10	ENST00000690296.1	MANE Select	c.35-930G>A		intron	N/A	ENSP00000509702.1	Q8WWZ4-1
	ABCA10	ENST00000269081.8	TSL:1	c.35-930G>A		intron	N/A	ENSP00000269081.4	Q8WWZ4-1
	ABCA10	ENST00000518929.5	TSL:1	n.35-930G>A		intron	N/A	ENSP00000430341.1	E5RFP5

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29003 AN: 151976 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.181

GnomAD2 exomes AF: 0.125 AC: 13446 AN: 107788 AF XY: 0.119

Gnomad AFR exome AF: 0.352

Gnomad AMR exome AF: 0.154

Gnomad ASJ exome AF: 0.118

Gnomad EAS exome AF: 0.0329

Gnomad FIN exome AF: 0.136

Gnomad NFE exome AF: 0.124

Gnomad OTH exome AF: 0.129

GnomAD4 exome AF: 0.122 AC: 34510 AN: 283252 Hom.: 2456 Cov.: 0 AF XY: 0.116 AC XY: 18911 AN XY: 162774

African (AFR) AF: 0.337 AC: 2205 AN: 6534

American (AMR) AF: 0.155 AC: 3578 AN: 23148

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 1165 AN: 9970

East Asian (EAS) AF: 0.0306 AC: 237 AN: 7752

South Asian (SAS) AF: 0.0855 AC: 4851 AN: 56718

European-Finnish (FIN) AF: 0.134 AC: 1608 AN: 12016

Middle Eastern (MID) AF: 0.139 AC: 372 AN: 2672

European-Non Finnish (NFE) AF: 0.123 AC: 18625 AN: 151206

Other (OTH) AF: 0.141 AC: 1869 AN: 13236

GnomAD4 genome AF: 0.191 AC: 29044 AN: 152094 Hom.: 3656 Cov.: 32 AF XY: 0.188 AC XY: 13957 AN XY: 74362

African (AFR) AF: 0.352 AC: 14601 AN: 41436

American (AMR) AF: 0.182 AC: 2776 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5188

South Asian (SAS) AF: 0.0797 AC: 385 AN: 4828

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8801 AN: 67990

Other (OTH) AF: 0.180 AC: 380 AN: 2112

Alfa AF: 0.141 Hom.: 3617

Bravo AF: 0.205

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-0.86
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: rs1468512; hg19: chr17-67219768;