rs75363899

Positions:

• chr18-656356-C-T

Variant summary

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

The NR_171001.1(TYMSOS):​n.450+1486G>A 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 0.0227 in 152,234 control chromosomes in the GnomAD database, including 101 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 0.023 (101 hom., cov: 31)
• Consequence: TYMSOS NR_171001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TYMSOS	NR_171001.1	n.450+1486G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000584679.1	n.38+866G>A		intron_variant, non_coding_transcript_variant		3
TYMSOS	ENST00000585033.1	n.428+1486G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0226 AC: 3438 AN: 152116 Hom.: 101 Cov.: 31

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00714

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000617

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0227 AC: 3453 AN: 152234 Hom.: 101 Cov.: 31 AF XY: 0.0237 AC XY: 1767 AN XY: 74430

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.00713

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0972

Gnomad4 SAS AF: 0.0256

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.000617

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.0169 Hom.: 6

Bravo AF: 0.0240

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75363899; hg19: chr18-656356;