Genetic Variant TYMSOS:n.511+490A>T (chr18-657352-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000323813.6(TYMSOS):n.511+490A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TYMSOS
ENST00000323813.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.883

Publications

30 publications found

Variant links:

Genes affected

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

TYMSOS links:

ENSG00000263727 (HGNC:):

ENSG00000263727 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYMSOS	NR_171001.1 link	n.450+490A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TYMSOS	ENST00000323813.6 link	n.511+490A>T	intron_variant	Intron 1 of 1	1
TYMSOS	ENST00000701410.1 link	n.245A>T	non_coding_transcript_exon_variant	Exon 1 of 2
TYMSOS	ENST00000585033.1 link	n.428+490A>T	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

21448

Hom.:

AF XY:

0.00

AC XY:

AN XY:

10876

African (AFR)

AF:

0.00

AC:

AN:

776

American (AMR)

AF:

0.00

AC:

AN:

552

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

916

East Asian (EAS)

AF:

0.00

AC:

AN:

1004

South Asian (SAS)

AF:

0.00

AC:

AN:

218

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1752

Middle Eastern (MID)

AF:

0.00

AC:

AN:

120

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

14604

Other (OTH)

AF:

0.00

AC:

AN:

1506

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.6

(source)

DANN

Benign

0.63

PhyloP100

0.88

PromoterAI

-0.011

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.97

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over