chr10-5739665-T-G

Position:

• chr10-5739665-T-G

Variant summary

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

The NM_001321783.2(TASOR2):​c.1495T>G​(p.Cys499Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 1,613,460 control chromosomes in the GnomAD database, including 563,167 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.85 (54806 hom., cov: 30)
  • Exomes 𝑓: 0.83 (508361 hom.)
• Consequence: TASOR2 NM_001321783.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

Genes affected

TASOR2 (HGNC:23484): (transcription activation suppressor family member 2) Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TASOR2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.1235861E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TASOR2	NM_001321783.2	c.1495T>G	p.Cys499Gly	missense_variant	14/22	ENST00000695737.1	NP_001308712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TASOR2	ENST00000695737.1	c.1495T>G	p.Cys499Gly	missense_variant	14/22		NM_001321783.2	ENSP00000512130.1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128918 AN: 151956 Hom.: 54765 Cov.: 30

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.842

GnomAD3 exomes AF: 0.838 AC: 209041 AN: 249342 Hom.: 87787 AF XY: 0.833 AC XY: 112701 AN XY: 135294

Gnomad AFR exome AF: 0.874

Gnomad AMR exome AF: 0.903

Gnomad ASJ exome AF: 0.766

Gnomad EAS exome AF: 0.809

Gnomad SAS exome AF: 0.783

Gnomad FIN exome AF: 0.872

Gnomad NFE exome AF: 0.833

Gnomad OTH exome AF: 0.836

GnomAD4 exome AF: 0.833 AC: 1217964 AN: 1461386 Hom.: 508361 Cov.: 47 AF XY: 0.831 AC XY: 603869 AN XY: 726938

Gnomad4 AFR exome AF: 0.879

Gnomad4 AMR exome AF: 0.902

Gnomad4 ASJ exome AF: 0.779

Gnomad4 EAS exome AF: 0.790

Gnomad4 SAS exome AF: 0.780

Gnomad4 FIN exome AF: 0.867

Gnomad4 NFE exome AF: 0.835

Gnomad4 OTH exome AF: 0.827

GnomAD4 genome AF: 0.848 AC: 129012 AN: 152074 Hom.: 54806 Cov.: 30 AF XY: 0.850 AC XY: 63154 AN XY: 74330

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.836

Alfa AF: 0.834 Hom.: 111268

Bravo AF: 0.852

TwinsUK AF: 0.835 AC: 3097

ALSPAC AF: 0.834 AC: 3216

ESP6500AA AF: 0.871 AC: 3240

ESP6500EA AF: 0.832 AC: 6829

ExAC AF: 0.837 AC: 101038

Asia WGS AF: 0.783 AC: 2721 AN: 3478

EpiCase AF: 0.830

EpiControl AF: 0.828

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.051
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	3.7
DANN	Benign	0.50
DEOGEN2	Benign	0.0010	T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.00073	N
LIST_S2	Benign	0.28	T;T
MetaRNN	Benign	0.0000011	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.2	N;.
PrimateAI	Benign	0.28	T
PROVEAN	Benign	2.2	N;.
REVEL	Benign	0.20
Sift	Benign	1.0	T;.
Sift4G	Benign	1.0	T;.
Polyphen		0.0	B;.
Vest4		0.018
MPC		0.050
ClinPred		0.00053	T
GERP RS		2.4
Varity_R		0.026
gMVP		0.092

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: rs2254067; hg19: chr10-5781628;