rs2822558

Positions:

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

Variant summary

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

The ENST00000467409.6(ABCC13):​n.933G>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 ENST00000467409.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

ABCC13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC13	NR_003087.1	n.976G>A		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000467409.6	n.933G>A		non_coding_transcript_exon_variant	6/6	1
ABCC13	ENST00000481582.5	n.3918G>A		non_coding_transcript_exon_variant	5/5	1
ABCC13	ENST00000482980.5	n.891-6173G>A		intron_variant		1

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

GnomAD3 exomes AF: 0.122 AC: 17074 AN: 139554 Hom.: 1273 AF XY: 0.124 AC XY: 9402 AN XY: 75632

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 SAS exome AF: 0.122

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

Gnomad4 AFR exome AF: 0.0585

Gnomad4 AMR exome AF: 0.0729

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.00923

Gnomad4 SAS exome AF: 0.120

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.138

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

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.121

Alfa AF: 0.148 Hom.: 2880

Bravo AF: 0.110

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822558; hg19: chr21-15671844;