rs365433

Variant names:

• chr21-14259892-T-C
• rs365433
• ENST00000429114.5:n.102-8511T>C

Variant summary

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

The ENST00000429114.5(ABCC13):​n.102-8511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,018 control chromosomes in the GnomAD database, including 20,424 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 0.52 (20424 hom., cov: 32)
• Consequence: ABCC13 ENST00000429114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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.102-8511T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78329 AN: 151900 Hom.: 20414 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.515 AC: 78363 AN: 152018 Hom.: 20424 Cov.: 32 AF XY: 0.516 AC XY: 38377 AN XY: 74316

African (AFR) AF: 0.432 AC: 17913 AN: 41434

American (AMR) AF: 0.486 AC: 7423 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2071 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3002 AN: 5170

South Asian (SAS) AF: 0.577 AC: 2783 AN: 4826

European-Finnish (FIN) AF: 0.536 AC: 5666 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37608 AN: 67948

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.519 Hom.: 2686

Bravo AF: 0.510

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.81
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs365433; hg19: chr21-15632213;