3-56627292-T-G

Variant names:

• chr3-56627292-T-G
• rs2029464
• NM_001365635.2:c.4031-147A>C

Variant summary

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

The NM_001365635.2(TASOR):​c.4031-147A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 625,802 control chromosomes in the GnomAD database, including 28,178 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 0.32 (8079 hom., cov: 33)
  • Exomes 𝑓: 0.28 (20099 hom.)
• Consequence: TASOR NM_001365635.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TASOR	NM_001365635.2	c.4031-147A>C		intron_variant	Intron 20 of 23	ENST00000683822.1	NP_001352564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TASOR	ENST00000683822.1	c.4031-147A>C		intron_variant	Intron 20 of 23		NM_001365635.2	ENSP00000508241.1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48202 AN: 151970 Hom.: 8075 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.281 AC: 133051 AN: 473716 Hom.: 20099 AF XY: 0.276 AC XY: 69076 AN XY: 250516

African (AFR) AF: 0.364 AC: 4633 AN: 12738

American (AMR) AF: 0.455 AC: 8413 AN: 18486

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 3164 AN: 13876

East Asian (EAS) AF: 0.463 AC: 14464 AN: 31220

South Asian (SAS) AF: 0.233 AC: 10297 AN: 44260

European-Finnish (FIN) AF: 0.294 AC: 10117 AN: 34422

Middle Eastern (MID) AF: 0.169 AC: 341 AN: 2012

European-Non Finnish (NFE) AF: 0.255 AC: 73890 AN: 289916

Other (OTH) AF: 0.289 AC: 7732 AN: 26786

GnomAD4 genome AF: 0.317 AC: 48242 AN: 152086 Hom.: 8079 Cov.: 33 AF XY: 0.321 AC XY: 23878 AN XY: 74344

African (AFR) AF: 0.372 AC: 15424 AN: 41476

American (AMR) AF: 0.435 AC: 6653 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2520 AN: 5178

South Asian (SAS) AF: 0.239 AC: 1156 AN: 4830

European-Finnish (FIN) AF: 0.311 AC: 3277 AN: 10548

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17446 AN: 67982

Other (OTH) AF: 0.315 AC: 665 AN: 2114

Alfa AF: 0.244 Hom.: 2561

Bravo AF: 0.332

Asia WGS AF: 0.361 AC: 1255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2029464; hg19: chr3-56661320;