rs10916508

Positions:

• chr1-229524044-T-C

Variant summary

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

The NM_012089.3(ABCB10):​c.1906+1892A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,950 control chromosomes in the GnomAD database, including 4,117 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 0.23 (4117 hom., cov: 31)
• Consequence: ABCB10 NM_012089.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

Genes affected

ABCB10 (HGNC:41): (ATP binding cassette subfamily B 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 intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The function of this mitochondrial protein is unknown. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB10	NM_012089.3	c.1906+1892A>G		intron_variant		ENST00000344517.5
ABCB10	XM_011544135.4	c.1369+1892A>G		intron_variant
ABCB10	XM_011544136.2	c.1018+1892A>G		intron_variant
ABCB10	XM_047416589.1	c.1369+1892A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB10	ENST00000344517.5	c.1906+1892A>G		intron_variant		1	NM_012089.3	P1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34616 AN: 151838 Hom.: 4105 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.228 AC: 34649 AN: 151950 Hom.: 4117 Cov.: 31 AF XY: 0.223 AC XY: 16579 AN XY: 74256

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.267

Alfa AF: 0.230 Hom.: 2382

Bravo AF: 0.241

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.76

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: rs10916508; hg19: chr1-229659791;