ENST00000323813.6:n.512-3262T>G

Variant names:

• chr18-653226-A-C
• rs36124867
• ENST00000323813.6:n.512-3262T>G

Variant summary

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

The ENST00000323813.6(TYMSOS):​n.512-3262T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,046 control chromosomes in the GnomAD database, including 4,411 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 0.24 (4411 hom., cov: 32)
• Consequence: TYMSOS ENST00000323813.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYMSOS	NR_171001.1	n.451-3262T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYMSOS	ENST00000323813.6	n.512-3262T>G		intron_variant	Intron 1 of 1	1
TYMSOS	ENST00000585033.1	n.428+4616T>G		intron_variant	Intron 1 of 1	2
TYMSOS	ENST00000688530.2	n.283-3262T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35934 AN: 151928 Hom.: 4408 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.237 AC: 35978 AN: 152046 Hom.: 4411 Cov.: 32 AF XY: 0.241 AC XY: 17877 AN XY: 74320

African (AFR) AF: 0.205 AC: 8522 AN: 41514

American (AMR) AF: 0.236 AC: 3612 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3468

East Asian (EAS) AF: 0.0950 AC: 493 AN: 5188

South Asian (SAS) AF: 0.199 AC: 960 AN: 4824

European-Finnish (FIN) AF: 0.368 AC: 3858 AN: 10492

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17109 AN: 67974

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.251 Hom.: 623

Bravo AF: 0.226

Asia WGS AF: 0.139 AC: 479 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		0.049
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: rs36124867; hg19: chr18-653226;