rs365433

Positions:

• chr21-14259892-T-C

Variant summary

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

The ENST00000429114.5(ABCC13):​n.102-8511T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,018 control chromosomes in the GnomAD database, including 20,424 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 0.52 (20424 hom., cov: 32)
• Consequence: ABCC13 ENST00000429114.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

Genes affected

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000429114.5	n.102-8511T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78329 AN: 151900 Hom.: 20414 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.515 AC: 78363 AN: 152018 Hom.: 20424 Cov.: 32 AF XY: 0.516 AC XY: 38377 AN XY: 74316

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.542

Alfa AF: 0.523 Hom.: 2618

Bravo AF: 0.510

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs365433; hg19: chr21-15632213;