chr20-13212001-C-T

Variant names:

• chr20-13212001-C-T
• rs6105047
• XR_001754319.3:n.1369+103969G>A

Variant summary

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

The XR_001754319.3(TASP1):​n.1369+103969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,964 control chromosomes in the GnomAD database, including 18,617 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 0.47 (18617 hom., cov: 32)
• Consequence: TASP1 XR_001754319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

TASP1 (HGNC:15859): (taspase 1) This gene encodes an endopeptidase that cleaves specific substrates following aspartate residues. The encoded protein undergoes posttranslational autoproteolytic processing to generate alpha and beta subunits, which reassemble into the active alpha2-beta2 heterotetramer. It is required to cleave MLL, a protein required for the maintenance of HOX gene expression, and TFIIA, a basal transcription factor. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -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 = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TASP1	XR_001754319.3	n.1369+103969G>A		intron_variant	Intron 14 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71668 AN: 151846 Hom.: 18571 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.472 AC: 71771 AN: 151964 Hom.: 18617 Cov.: 32 AF XY: 0.466 AC XY: 34645 AN XY: 74270

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.434

Alfa AF: 0.397 Hom.: 5982

Bravo AF: 0.486

Asia WGS AF: 0.434 AC: 1509 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	0.18
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6105047; hg19: chr20-13192648;