rs2822558

Variant names:

• chr21-14299523-G-A
• rs2822558
• ENST00000467409.7:n.1041G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-14299523-G-A
• chr21-14299523-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000467409.7(ABCC13):​n.1041G>A 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 0.13 in 456,608 control chromosomes in the GnomAD database, including 4,480 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 0.12 (1235 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3245 hom.)
• Consequence: ABCC13 ENST00000467409.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 11 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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.976G>A		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC13	ENST00000467409.7	TSL:1	n.1041G>A		non_coding_transcript_exon	Exon 6 of 6
	ABCC13	ENST00000481582.5	TSL:1	n.3918G>A		non_coding_transcript_exon	Exon 5 of 5
	ABCC13	ENST00000482980.5	TSL:1	n.891-6173G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18143 AN: 152074 Hom.: 1235 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.122

GnomAD2 exomes AF: 0.122 AC: 17074 AN: 139554 AF XY: 0.124

Gnomad AFR exome AF: 0.0578

Gnomad AMR exome AF: 0.0750

Gnomad ASJ exome AF: 0.189

Gnomad EAS exome AF: 0.00847

Gnomad FIN exome AF: 0.166

Gnomad NFE exome AF: 0.156

Gnomad OTH exome AF: 0.134

GnomAD4 exome AF: 0.136 AC: 41390 AN: 304416 Hom.: 3245 Cov.: 0 AF XY: 0.135 AC XY: 23410 AN XY: 173340

African (AFR) AF: 0.0585 AC: 505 AN: 8626

American (AMR) AF: 0.0729 AC: 1990 AN: 27280

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 2079 AN: 10790

East Asian (EAS) AF: 0.00923 AC: 85 AN: 9210

South Asian (SAS) AF: 0.120 AC: 7151 AN: 59738

European-Finnish (FIN) AF: 0.171 AC: 2194 AN: 12796

Middle Eastern (MID) AF: 0.145 AC: 403 AN: 2784

European-Non Finnish (NFE) AF: 0.157 AC: 25015 AN: 158948

Other (OTH) AF: 0.138 AC: 1968 AN: 14244

GnomAD4 genome AF: 0.119 AC: 18136 AN: 152192 Hom.: 1235 Cov.: 32 AF XY: 0.118 AC XY: 8761 AN XY: 74406

African (AFR) AF: 0.0623 AC: 2586 AN: 41522

American (AMR) AF: 0.100 AC: 1529 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3468

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5186

South Asian (SAS) AF: 0.114 AC: 549 AN: 4826

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10555 AN: 68014

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.144 Hom.: 4533

Bravo AF: 0.110

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.1
DANN	Benign	0.80
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2822558;

hg19: chr21-15671844;