rs2179593

Variant names:

• chr20-44031646-C-A
• rs2179593
• NM_001098797.2:c.412-19660C>A

Your query was ambiguous. Multiple possible variants found:

• chr20-44031646-C-A
• chr20-44031646-C-G

Variant summary

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

The NM_001098797.2(TOX2):​c.412-19660C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 151,734 control chromosomes in the GnomAD database, including 38,315 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 0.71 (38315 hom., cov: 29)
• Consequence: TOX2 NM_001098797.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804
• Publications: 4 publications found

Genes affected

TOX2 (HGNC:16095): (TOX high mobility group box family member 2) Enables transcription coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Located in 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098797.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOX2	NM_001098797.2	MANE Select	c.412-19660C>A		intron	N/A	NP_001092267.1	Q96NM4-4
	TOX2	NM_001098798.2		c.439-19660C>A		intron	N/A	NP_001092268.1	Q96NM4-1
	TOX2	NM_001098796.2		c.286-19660C>A		intron	N/A	NP_001092266.1	Q96NM4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOX2	ENST00000341197.9	TSL:2 MANE Select	c.412-19660C>A		intron	N/A	ENSP00000344724.3	Q96NM4-4
	TOX2	ENST00000372999.5	TSL:1	c.286-19660C>A		intron	N/A	ENSP00000362090.1	Q96NM4-3
	TOX2	ENST00000864666.1		c.412-19660C>A		intron	N/A	ENSP00000534725.1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107376 AN: 151616 Hom.: 38294 Cov.: 29

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.719

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.708 AC: 107451 AN: 151734 Hom.: 38315 Cov.: 29 AF XY: 0.708 AC XY: 52522 AN XY: 74132

African (AFR) AF: 0.690 AC: 28526 AN: 41330

American (AMR) AF: 0.686 AC: 10470 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2765 AN: 3472

East Asian (EAS) AF: 0.784 AC: 4036 AN: 5150

South Asian (SAS) AF: 0.576 AC: 2740 AN: 4754

European-Finnish (FIN) AF: 0.734 AC: 7738 AN: 10542

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48745 AN: 67926

Other (OTH) AF: 0.717 AC: 1508 AN: 2102

Alfa AF: 0.710 Hom.: 27859

Bravo AF: 0.707

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.80
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: rs2179593; hg19: chr20-42660286;