10-5762568-G-A

Variant names:

• chr10-5762568-G-A
• rs2797501
• NM_001321783.2:c.7211G>A

Variant summary

Our verdict is Benign. The variant received -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. 15/21 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: 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
• Publications: 40 publications found

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

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TASOR2	NM_001321783.2	MANE Select	c.7211G>A	p.Ser2404Asn	missense	Exon 21 of 22	NP_001308712.2
	TASOR2	NM_001387328.1		c.7856G>A	p.Ser2619Asn	missense	Exon 23 of 24	NP_001374257.1
	TASOR2	NM_001321784.2		c.7211G>A	p.Ser2404Asn	missense	Exon 21 of 22	NP_001308713.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TASOR2	ENST00000695737.1	MANE Select	c.7211G>A	p.Ser2404Asn	missense	Exon 21 of 22	ENSP00000512130.1
	TASOR2	ENST00000328090.9	TSL:1	c.7211G>A	p.Ser2404Asn	missense	Exon 20 of 21	ENSP00000328426.5
	TASOR2	ENST00000459693.1	TSL:1	n.669G>A		non_coding_transcript_exon	Exon 2 of 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

GnomAD2 exomes AF: 0.850 AC: 157589 AN: 185398 AF XY: 0.848

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 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

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

African (AFR) AF: 0.862 AC: 21490 AN: 24916

American (AMR) AF: 0.912 AC: 24437 AN: 26802

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 18133 AN: 22712

East Asian (EAS) AF: 0.779 AC: 25791 AN: 33100

South Asian (SAS) AF: 0.805 AC: 54525 AN: 67768

European-Finnish (FIN) AF: 0.872 AC: 44416 AN: 50942

Middle Eastern (MID) AF: 0.834 AC: 4185 AN: 5018

European-Non Finnish (NFE) AF: 0.857 AC: 804529 AN: 938450

Other (OTH) AF: 0.845 AC: 43140 AN: 51074

⚠️ 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.

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

African (AFR) AF: 0.872 AC: 35228 AN: 40402

American (AMR) AF: 0.891 AC: 13362 AN: 15004

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2781 AN: 3468

East Asian (EAS) AF: 0.814 AC: 4142 AN: 5088

South Asian (SAS) AF: 0.813 AC: 3845 AN: 4732

European-Finnish (FIN) AF: 0.883 AC: 8451 AN: 9568

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.864 AC: 58463 AN: 67688

Other (OTH) AF: 0.861 AC: 1768 AN: 2054

Alfa AF: 0.861 Hom.: 181383

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 v4.9

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
MetaRNN	Benign	6.7e-7	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.67	N
PhyloP100		0.21
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
Mutation Taster		=99/1	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: rs2797501; hg19: chr10-5804531; COSMIC: COSV108110053; COSMIC: COSV108110053;