3-56623229-C-T

Position:

• chr3-56623229-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001365635.2(TASOR):​c.4821G>A​(p.Gln1607=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 1,613,328 control chromosomes in the GnomAD database, including 318 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 0.027 (97 hom., cov: 32)
  • Exomes 𝑓: 0.015 (221 hom.)
• Consequence: TASOR NM_001365635.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

Genes affected

TASOR (HGNC:30314): (transcription activation suppressor) Enables chromatin binding activity. Involved in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; protein localization to heterochromatin; and regulation of gene expression. Located in heterochromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BP7: Synonymous conserved (PhyloP=0.361 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TASOR	NM_001365635.2	c.4821G>A	p.Gln1607=	synonymous_variant	24/24	ENST00000683822.1	NP_001352564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TASOR	ENST00000683822.1	c.4821G>A	p.Gln1607=	synonymous_variant	24/24		NM_001365635.2	ENSP00000508241	A2

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4047 AN: 152110 Hom.: 94 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0132

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.00462

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0259

GnomAD3 exomes AF: 0.0155 AC: 3891 AN: 250750 Hom.: 60 AF XY: 0.0156 AC XY: 2108 AN XY: 135522

Gnomad AFR exome AF: 0.0601

Gnomad AMR exome AF: 0.00985

Gnomad ASJ exome AF: 0.0152

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.0146

Gnomad FIN exome AF: 0.00464

Gnomad NFE exome AF: 0.0156

Gnomad OTH exome AF: 0.0167

GnomAD4 exome AF: 0.0148 AC: 21596 AN: 1461100 Hom.: 221 Cov.: 32 AF XY: 0.0149 AC XY: 10812 AN XY: 726850

Gnomad4 AFR exome AF: 0.0630

Gnomad4 AMR exome AF: 0.0109

Gnomad4 ASJ exome AF: 0.0154

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0157

Gnomad4 FIN exome AF: 0.00538

Gnomad4 NFE exome AF: 0.0142

Gnomad4 OTH exome AF: 0.0171

GnomAD4 genome AF: 0.0268 AC: 4074 AN: 152228 Hom.: 97 Cov.: 32 AF XY: 0.0261 AC XY: 1945 AN XY: 74430

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.0132

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.00462

Gnomad4 NFE AF: 0.0149

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.0178 Hom.: 66

Bravo AF: 0.0284

Asia WGS AF: 0.0180 AC: 63 AN: 3478

EpiCase AF: 0.0190

EpiControl AF: 0.0190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	4.0
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510787; hg19: chr3-56657257;