chr1-229524044-T-C

Variant names:

• chr1-229524044-T-C
• rs10916508
• NM_012089.3:c.1906+1892A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012089.3. 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
	ABCB10	NM_012089.3	MANE Select	c.1906+1892A>G		intron	N/A	NP_036221.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB10	ENST00000344517.5	TSL:1 MANE Select	c.1906+1892A>G		intron	N/A	ENSP00000355637.3

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

African (AFR) AF: 0.239 AC: 9896 AN: 41424

American (AMR) AF: 0.263 AC: 4007 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.155 AC: 804 AN: 5174

South Asian (SAS) AF: 0.160 AC: 771 AN: 4808

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15503 AN: 67964

Other (OTH) AF: 0.267 AC: 563 AN: 2106

Alfa AF: 0.232 Hom.: 2632

Bravo AF: 0.241

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		0.50
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: rs10916508; hg19: chr1-229659791;