21-14348082-A-G

Position:

• chr21-14348082-A-G

Variant summary

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

The ENST00000463099.1(ABCC13):​n.2558A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,472 control chromosomes in the GnomAD database, including 10,371 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 0.35 (10358 hom., cov: 32)
  • Exomes 𝑓: 0.23 (13 hom.)
• Consequence: ABCC13 ENST00000463099.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC13	ENST00000463099.1	n.2558A>G		non_coding_transcript_exon_variant	20/28

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53782 AN: 151922 Hom.: 10340 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.229 AC: 99 AN: 432 Hom.: 13 Cov.: 0 AF XY: 0.208 AC XY: 54 AN XY: 260

Gnomad4 FIN exome AF: 0.225

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.354 AC: 53837 AN: 152040 Hom.: 10358 Cov.: 32 AF XY: 0.350 AC XY: 26012 AN XY: 74330

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.350

Alfa AF: 0.306 Hom.: 3901

Bravo AF: 0.365

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822612; hg19: chr21-15720403;