20-13210262-T-C

Position:

• chr20-13210262-T-C

Variant summary

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

The XR_001754319.3(TASP1):​n.1370-105005A>G 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 0.469 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

TASP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASP1	XR_001754319.3	n.1370-105005A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.430

Alfa AF: 0.366 Hom.: 4432

Bravo AF: 0.480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6109753; hg19: chr20-13190909;