rs380011

Variant names:

• chr21-14248477-T-C
• rs380011
• ENST00000429114.5:n.101+12171T>C

Variant summary

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

The ENST00000429114.5(ABCC13):​n.101+12171T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,038 control chromosomes in the GnomAD database, including 12,595 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 0.41 (12595 hom., cov: 32)
• Consequence: ABCC13 ENST00000429114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 7 publications found

Genes affected

ABCC13 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000429114.5	n.101+12171T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61636 AN: 151920 Hom.: 12568 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.406 AC: 61715 AN: 152038 Hom.: 12595 Cov.: 32 AF XY: 0.407 AC XY: 30227 AN XY: 74342

African (AFR) AF: 0.453 AC: 18800 AN: 41456

American (AMR) AF: 0.369 AC: 5641 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2310 AN: 5176

South Asian (SAS) AF: 0.406 AC: 1956 AN: 4812

European-Finnish (FIN) AF: 0.398 AC: 4210 AN: 10574

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26115 AN: 67958

Other (OTH) AF: 0.391 AC: 823 AN: 2104

Alfa AF: 0.391 Hom.: 16699

Bravo AF: 0.406

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.98
DANN	Benign	0.73
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs380011; hg19: chr21-15620798;