8-59120246-T-G

Variant names:

• chr8-59120246-T-G
• rs2290526
• ENST00000688120.1:n.379T>G

Variant summary

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

The ENST00000688120.1(TOX-DT):​n.379T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,666 control chromosomes in the GnomAD database, including 1,309 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 0.11 (1296 hom., cov: 32)
  • Exomes 𝑓: 0.18 (13 hom.)
• Consequence: TOX-DT ENST00000688120.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

TOX-DT (HGNC:55935): (TOX divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOX-DT	NR_149030.1	n.77-90T>G		intron_variant	Intron 1 of 1
TOX-DT	NR_149031.1	n.192-90T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOX-DT	ENST00000688120.1	n.379T>G		non_coding_transcript_exon_variant	Exon 1 of 1
TOX-DT	ENST00000517898.1	n.127-90T>G		intron_variant	Intron 1 of 1	2
TOX-DT	ENST00000518993.2	n.77-90T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16959 AN: 152014 Hom.: 1297 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.182 AC: 97 AN: 534 Hom.: 13 Cov.: 0 AF XY: 0.172 AC XY: 58 AN XY: 338

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.193

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.111 AC: 16961 AN: 152132 Hom.: 1296 Cov.: 32 AF XY: 0.117 AC XY: 8681 AN XY: 74370

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.126

Alfa AF: 0.105 Hom.: 968

Bravo AF: 0.110

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2290526; hg19: chr8-60032805; COSMIC: COSV63852091;