rs1923342

chr20-13199985-G-Achr20-13199985-G-C

Variant summary

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

The XR_001754319.3(TASP1):n.1370-94728C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

TASP1 (HGNC:):

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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASP1	XR_001754319.3	n.1370-94728C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.421

Alfa AF: 0.382 Hom.: 5675

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923342; hg19: chr20-13180632;