rs8088001

Variant names:

• chr18-287705-T-G
• rs8088001
• ENST00000819908.1:n.632-4889T>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.632-4889T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,108 control chromosomes in the GnomAD database, including 2,121 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 0.14 (2121 hom., cov: 32)
• Consequence: THOC1-DT ENST00000819908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THOC1-DT	ENST00000819908.1		n.632-4889T>G		intron	N/A
	THOC1-DT	ENST00000819909.1		n.762-4889T>G		intron	N/A
	THOC1-DT	ENST00000819910.1		n.68-4889T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20791 AN: 151990 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.137 AC: 20825 AN: 152108 Hom.: 2121 Cov.: 32 AF XY: 0.140 AC XY: 10395 AN XY: 74372

African (AFR) AF: 0.280 AC: 11596 AN: 41450

American (AMR) AF: 0.0785 AC: 1200 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0900 AC: 312 AN: 3468

East Asian (EAS) AF: 0.0413 AC: 214 AN: 5184

South Asian (SAS) AF: 0.160 AC: 769 AN: 4818

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0757 AC: 5146 AN: 67996

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.0935 Hom.: 1907

Bravo AF: 0.139

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.22
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs8088001; hg19: chr18-287705;