21-14285390-T-G

Variant names:

• chr21-14285390-T-G
• rs1153303
• ENST00000467409.7:n.487-2160T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000467409.7(ABCC13):​n.487-2160T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,204 control chromosomes in the GnomAD database, including 52,235 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 0.82 (52235 hom., cov: 34)
• Consequence: ABCC13 ENST00000467409.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 4 publications found

Genes affected

ABCC13 (HGNC:):

ABCC13 (HGNC:16022): (ATP binding cassette subfamily C member 13 (pseudogene)) This gene is a member of the superfamily of genes encoding 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, and White). This family member is part of the MRP subfamily, which is involved in multi-drug resistance, but the human locus is now thought to be a pseudogene incapable of encoding a functional ABC protein. Alternative splicing results in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467409.7. 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
	ABCC13	NR_003087.1		n.422-2160T>G		intron	N/A
	ABCC13	NR_003088.1		n.422-2160T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC13	ENST00000467409.7	TSL:1	n.487-2160T>G		intron	N/A
	ABCC13	ENST00000471902.6	TSL:1	n.452-2160T>G		intron	N/A
	ABCC13	ENST00000481582.5	TSL:1	n.341-2160T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125418 AN: 152086 Hom.: 52186 Cov.: 34

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.825 AC: 125517 AN: 152204 Hom.: 52235 Cov.: 34 AF XY: 0.820 AC XY: 60982 AN XY: 74398

African (AFR) AF: 0.928 AC: 38543 AN: 41528

American (AMR) AF: 0.703 AC: 10744 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3134 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3481 AN: 5172

South Asian (SAS) AF: 0.772 AC: 3731 AN: 4832

European-Finnish (FIN) AF: 0.789 AC: 8338 AN: 10574

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54747 AN: 68018

Other (OTH) AF: 0.830 AC: 1757 AN: 2116

Alfa AF: 0.811 Hom.: 207170

Bravo AF: 0.822

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	18
DANN	Benign	0.74
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1153303; hg19: chr21-15657711;