chr18-655875-C-T

Variant names:

• chr18-655875-C-T
• rs58808873
• ENST00000323813.6:n.511+1967G>A

Variant summary

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

The ENST00000323813.6(TYMSOS):​n.511+1967G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0808 in 152,034 control chromosomes in the GnomAD database, including 658 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 0.081 (658 hom., cov: 31)
• Consequence: TYMSOS ENST00000323813.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 3 publications found

Genes affected

TYMSOS (HGNC:29553): (TYMS opposite strand RNA)

ENSG00000263727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYMSOS	NR_171001.1	n.450+1967G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYMSOS	ENST00000323813.6	n.511+1967G>A		intron_variant	Intron 1 of 1	1
ENSG00000263727	ENST00000584679.1	n.38+1347G>A		intron_variant	Intron 1 of 1	3
TYMSOS	ENST00000585033.1	n.428+1967G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12271 AN: 151916 Hom.: 659 Cov.: 31

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0808 AC: 12288 AN: 152034 Hom.: 658 Cov.: 31 AF XY: 0.0820 AC XY: 6092 AN XY: 74328

African (AFR) AF: 0.0954 AC: 3949 AN: 41408

American (AMR) AF: 0.0613 AC: 937 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3464

East Asian (EAS) AF: 0.180 AC: 928 AN: 5166

South Asian (SAS) AF: 0.202 AC: 973 AN: 4816

European-Finnish (FIN) AF: 0.0539 AC: 571 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0632 AC: 4295 AN: 68006

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.0388 Hom.: 34

Bravo AF: 0.0794

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.4
DANN	Benign	0.84
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs58808873; hg19: chr18-655875;