rs36124867

chr18-653226-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_171001.1(TYMSOS):n.451-3262T>G variant causes a intron, non coding transcript 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 NR_171001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TYMSOS	NR_171001.1	n.451-3262T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TYMSOS	ENST00000585033.1	n.428+4616T>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.216

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36124867; hg19: chr18-653226;