rs2822524

Positions:

• chr21-14276164-G-T
• chr21-14276164-G-A

Variant summary

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

The ENST00000467409.6(ABCC13):​n.316+2007G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,866 control chromosomes in the GnomAD database, including 14,784 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 0.43 (14784 hom., cov: 31)
• Consequence: ABCC13 ENST00000467409.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

ABCC13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC13	NR_003087.1	n.359+2007G>T		intron_variant
ABCC13	NR_003088.1	n.359+2007G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000467409.6	n.316+2007G>T		intron_variant		1
ABCC13	ENST00000471902.5	n.222+2007G>T		intron_variant		1
ABCC13	ENST00000481582.5	n.278+2007G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65816 AN: 151748 Hom.: 14776 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.434 AC: 65840 AN: 151866 Hom.: 14784 Cov.: 31 AF XY: 0.430 AC XY: 31911 AN XY: 74222

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.440

Alfa AF: 0.478 Hom.: 23429

Bravo AF: 0.419

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822524; hg19: chr21-15648485;