XR_001754319.3:n.1370-94728C>T

Variant names:

• chr20-13199985-G-A
• rs1923342
• XR_001754319.3:n.1370-94728C>T

Variant summary

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

The XR_001754319.3(TASP1):​n.1370-94728C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,070 control chromosomes in the GnomAD database, including 19,114 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 (19114 hom., cov: 33)
• Consequence: TASP1 XR_001754319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 1 publications found

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]

TASP1 Gene-Disease associations (from GenCC):

• Suleiman-El-Hattab syndrome

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P

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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TASP1	XR_001754319.3	n.1370-94728C>T		intron_variant	Intron 14 of 14

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71446 AN: 151952 Hom.: 19067 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.471 AC: 71551 AN: 152070 Hom.: 19114 Cov.: 33 AF XY: 0.465 AC XY: 34600 AN XY: 74340

African (AFR) AF: 0.743 AC: 30821 AN: 41488

American (AMR) AF: 0.373 AC: 5697 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2831 AN: 5184

South Asian (SAS) AF: 0.324 AC: 1564 AN: 4824

European-Finnish (FIN) AF: 0.370 AC: 3897 AN: 10534

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24710 AN: 67978

Other (OTH) AF: 0.421 AC: 887 AN: 2106

Alfa AF: 0.379 Hom.: 6172

Bravo AF: 0.486

Asia WGS AF: 0.430 AC: 1494 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	0.69
DANN	Benign	0.28
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs1923342; hg19: chr20-13180632;