rs6130511

Variant names:

• chr20-44052448-G-A
• rs6130511
• NM_001098797.2:c.651+903G>A

Variant summary

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

The NM_001098797.2(TOX2):​c.651+903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0618 in 152,234 control chromosomes in the GnomAD database, including 364 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 0.062 (364 hom., cov: 32)
• Consequence: TOX2 NM_001098797.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 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.651+903G>A		intron	N/A	NP_001092267.1	Q96NM4-4
	TOX2	NM_001098798.2		c.678+903G>A		intron	N/A	NP_001092268.1	Q96NM4-1
	TOX2	NM_001098796.2		c.525+903G>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.651+903G>A		intron	N/A	ENSP00000344724.3	Q96NM4-4
	TOX2	ENST00000372999.5	TSL:1	c.525+903G>A		intron	N/A	ENSP00000362090.1	Q96NM4-3
	TOX2	ENST00000864666.1		c.651+903G>A		intron	N/A	ENSP00000534725.1

Frequencies

GnomAD3 genomes AF: 0.0619 AC: 9414 AN: 152116 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0618 AC: 9414 AN: 152234 Hom.: 364 Cov.: 32 AF XY: 0.0630 AC XY: 4692 AN XY: 74420

African (AFR) AF: 0.0265 AC: 1103 AN: 41552

American (AMR) AF: 0.0677 AC: 1035 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.131 AC: 674 AN: 5164

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4824

European-Finnish (FIN) AF: 0.0948 AC: 1004 AN: 10596

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0715 AC: 4861 AN: 68008

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

Alfa AF: 0.0657 Hom.: 718

Bravo AF: 0.0579

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.70
PhyloP100		0.078
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: rs6130511; hg19: chr20-42681088;