10-5762568-G-A

Position:

• chr10-5762568-G-A

Variant summary

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

The NM_001321783.2(TASOR2):​c.7211G>A​(p.Ser2404Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 1,369,984 control chromosomes in the GnomAD database, including 500,691 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.86 (55859 hom., cov: 24)
  • Exomes 𝑓: 0.85 (444832 hom.)
• Consequence: TASOR2 NM_001321783.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=6.732448E-7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TASOR2	NM_001321783.2	c.7211G>A	p.Ser2404Asn	missense_variant	21/22	ENST00000695737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TASOR2	ENST00000695737.1	c.7211G>A	p.Ser2404Asn	missense_variant	21/22		NM_001321783.2

Frequencies

GnomAD3 genomes AF: 0.865 AC: 128959 AN: 149092 Hom.: 55823 Cov.: 24

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.866

GnomAD3 exomes AF: 0.850 AC: 157589 AN: 185398 Hom.: 67166 AF XY: 0.848 AC XY: 87327 AN XY: 103028

Gnomad AFR exome AF: 0.853

Gnomad AMR exome AF: 0.912

Gnomad ASJ exome AF: 0.784

Gnomad EAS exome AF: 0.785

Gnomad SAS exome AF: 0.811

Gnomad FIN exome AF: 0.877

Gnomad NFE exome AF: 0.855

Gnomad OTH exome AF: 0.843

GnomAD4 exome AF: 0.852 AC: 1040646 AN: 1220782 Hom.: 444832 Cov.: 18 AF XY: 0.851 AC XY: 521365 AN XY: 612934

Gnomad4 AFR exome AF: 0.862

Gnomad4 AMR exome AF: 0.912

Gnomad4 ASJ exome AF: 0.798

Gnomad4 EAS exome AF: 0.779

Gnomad4 SAS exome AF: 0.805

Gnomad4 FIN exome AF: 0.872

Gnomad4 NFE exome AF: 0.857

Gnomad4 OTH exome AF: 0.845

GnomAD4 genome AF: 0.865 AC: 129041 AN: 149202 Hom.: 55859 Cov.: 24 AF XY: 0.866 AC XY: 62850 AN XY: 72610

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.861

Alfa AF: 0.861 Hom.: 133675

Bravo AF: 0.869

TwinsUK AF: 0.868 AC: 3218

ALSPAC AF: 0.867 AC: 3342

ESP6500AA AF: 0.860 AC: 3073

ESP6500EA AF: 0.859 AC: 6956

ExAC AF: 0.858 AC: 103626

Asia WGS AF: 0.799 AC: 2772 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.82	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.61
DEOGEN2	Benign	0.0010	T;.
Eigen	Benign	-0.86
Eigen_PC	Benign	-0.66
FATHMM_MKL	Benign	0.0079	N
LIST_S2	Benign	0.60	T;T
MetaRNN	Benign	6.7e-7	T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.67	N;.
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.30	T
PROVEAN	Benign	1.6	N;.
REVEL	Benign	0.031
Sift	Benign	0.77	T;.
Sift4G	Benign	0.37	T;.
Polyphen		0.034	B;.
Vest4		0.017
MPC		0.043
ClinPred		0.0016	T
GERP RS		-0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.047
gMVP		0.25

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: rs2797501; hg19: chr10-5804531;