18-278796-A-G

Variant names:

• chr18-278796-A-G
• rs7226677
• ENST00000819908.1:n.631+9923A>G

Variant summary

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

The ENST00000819908.1(THOC1-DT):​n.631+9923A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,178 control chromosomes in the GnomAD database, including 2,521 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 0.18 (2521 hom., cov: 33)
• Consequence: THOC1-DT ENST00000819908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 13 publications found

Genes affected

THOC1-DT (HGNC:55334): (THOC1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819908.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THOC1-DT	ENST00000819908.1		n.631+9923A>G		intron	N/A
	THOC1-DT	ENST00000819909.1		n.761+9923A>G		intron	N/A
	THOC1-DT	ENST00000819910.1		n.67+10618A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26643 AN: 152060 Hom.: 2517 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.175 AC: 26667 AN: 152178 Hom.: 2521 Cov.: 33 AF XY: 0.182 AC XY: 13563 AN XY: 74410

African (AFR) AF: 0.186 AC: 7729 AN: 41518

American (AMR) AF: 0.266 AC: 4068 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1685 AN: 5170

South Asian (SAS) AF: 0.208 AC: 1006 AN: 4834

European-Finnish (FIN) AF: 0.191 AC: 2018 AN: 10582

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9074 AN: 68008

Other (OTH) AF: 0.177 AC: 373 AN: 2106

Alfa AF: 0.153 Hom.: 6721

Bravo AF: 0.181

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs7226677; hg19: chr18-278796;