20-13210262-T-C

Variant names:

• chr20-13210262-T-C
• rs6109753
• XR_001754319.3:n.1370-105005A>G

Variant summary

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

The XR_001754319.3(TASP1):​n.1370-105005A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 150,948 control chromosomes in the GnomAD database, including 17,945 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 (17945 hom., cov: 32)
• Consequence: TASP1 XR_001754319.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.469 AC: 70715 AN: 150836 Hom.: 17912 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.469 AC: 70799 AN: 150948 Hom.: 17945 Cov.: 32 AF XY: 0.464 AC XY: 34180 AN XY: 73742

African (AFR) AF: 0.683 AC: 28319 AN: 41452

American (AMR) AF: 0.395 AC: 5865 AN: 14854

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 988 AN: 3458

East Asian (EAS) AF: 0.555 AC: 2865 AN: 5158

South Asian (SAS) AF: 0.326 AC: 1560 AN: 4778

European-Finnish (FIN) AF: 0.379 AC: 3941 AN: 10402

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26027 AN: 67552

Other (OTH) AF: 0.430 AC: 897 AN: 2088

Alfa AF: 0.371 Hom.: 5192

Bravo AF: 0.480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.36
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6109753; hg19: chr20-13190909;