rs6074591

chr20-13331336-C-T

Variant summary

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

The XM_047440269.1(TASP1):c.1171-15281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,190 control chromosomes in the GnomAD database, including 1,380 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 0.11 (1380 hom., cov: 32)
• Consequence: TASP1 XM_047440269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

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 (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASP1	XM_047440269.1	c.1171-15281G>A		intron_variant
TASP1	XR_001754319.3	n.1284-15281G>A		intron_variant, non_coding_transcript_variant
TASP1	XR_007067463.1	n.1284-15281G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17231 AN: 152072 Hom.: 1380 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.113 AC: 17231 AN: 152190 Hom.: 1380 Cov.: 32 AF XY: 0.111 AC XY: 8284 AN XY: 74386

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.104

Alfa AF: 0.147 Hom.: 281

Bravo AF: 0.102

Asia WGS AF: 0.0440 AC: 153 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	3.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6074591; hg19: chr20-13311983; COSMIC: COSV73356183;