ENST00000323813.6:n.511+1822G>C

Variant names:

• chr18-656020-C-G
• rs9967368
• ENST00000323813.6:n.511+1822G>C

Variant summary

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

The ENST00000323813.6(TYMSOS):​n.511+1822G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,742 control chromosomes in the GnomAD database, including 33,594 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 0.66 (33594 hom., cov: 30)
• Consequence: TYMSOS ENST00000323813.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYMSOS	NR_171001.1	n.450+1822G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYMSOS	ENST00000323813.6	n.511+1822G>C		intron_variant	Intron 1 of 1	1
ENSG00000263727	ENST00000584679.1	n.38+1202G>C		intron_variant	Intron 1 of 1	3
TYMSOS	ENST00000585033.1	n.428+1822G>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99985 AN: 151630 Hom.: 33542 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.660 AC: 100100 AN: 151742 Hom.: 33594 Cov.: 30 AF XY: 0.662 AC XY: 49071 AN XY: 74136

African (AFR) AF: 0.788 AC: 32618 AN: 41380

American (AMR) AF: 0.683 AC: 10420 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1983 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2272 AN: 5168

South Asian (SAS) AF: 0.590 AC: 2831 AN: 4798

European-Finnish (FIN) AF: 0.676 AC: 7092 AN: 10498

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40759 AN: 67876

Other (OTH) AF: 0.619 AC: 1302 AN: 2104

Alfa AF: 0.631 Hom.: 3570

Bravo AF: 0.666

Asia WGS AF: 0.528 AC: 1837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.49
PhyloP100		-1.7
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: rs9967368; hg19: chr18-656020;