Genetic Variant NM_001321783.2:c.7211G>C (chr10-5762568-G-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001321783.2(TASOR2):c.7211G>C(p.Ser2404Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000081 in 1,234,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 24)

Exomes 𝑓: 8.1e-7 ( 0 hom. )

Consequence

TASOR2
NM_001321783.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

40 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.13566673).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321783.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TASOR2	NM_001321783.2	MANE Select	c.7211G>C	p.Ser2404Thr	missense	Exon 21 of 22	NP_001308712.2	Q5VWN6-1
TASOR2	NM_001387328.1		c.7856G>C	p.Ser2619Thr	missense	Exon 23 of 24	NP_001374257.1	A0A2R8YH03
TASOR2	NM_001321784.2		c.7211G>C	p.Ser2404Thr	missense	Exon 21 of 22	NP_001308713.2	Q5VWN6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TASOR2	ENST00000695737.1	MANE Select	c.7211G>C	p.Ser2404Thr	missense	Exon 21 of 22	ENSP00000512130.1	Q5VWN6-1
TASOR2	ENST00000328090.9	TSL:1	c.7211G>C	p.Ser2404Thr	missense	Exon 20 of 21	ENSP00000328426.5	Q5VWN6-1
TASOR2	ENST00000459693.1	TSL:1	n.669G>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.10e-7

AC:

AN:

1234768

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

619706

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

25164

American (AMR)

AF:

0.00

AC:

AN:

26938

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22944

East Asian (EAS)

AF:

0.00

AC:

AN:

33398

South Asian (SAS)

AF:

0.00

AC:

AN:

68572

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51188

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5072

European-Non Finnish (NFE)

AF:

0.00000105

AC:

AN:

949846

Other (OTH)

AF:

0.00

AC:

AN:

51646

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.0034

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.18

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.70

M_CAP

Benign

0.0058

MetaRNN

Benign

0.14

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.7

PhyloP100

0.21

PrimateAI

Benign

0.28

PROVEAN

Benign

-1.5

REVEL

Benign

0.042

Sift

Uncertain

0.018

Sift4G

Benign

0.063

Polyphen

0.92

Vest4

0.25

MutPred

0.29

Loss of glycosylation at S2404 (P = 0.0174)

MVP

0.082

MPC

0.11

ClinPred

0.70

GERP RS

-0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.12

gMVP

0.31

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over