rs9967368

Positions:

• chr18-656020-C-G
• chr18-656020-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+1822G>C 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 0.66 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 NR_171001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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=-0.94).
• 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/exons	MANE	Protein	UniProt
TYMSOS	NR_171001.1	n.450+1822G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000584679.1	n.38+1202G>C		intron_variant, non_coding_transcript_variant		3
TYMSOS	ENST00000585033.1	n.428+1822G>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.619

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9967368; hg19: chr18-656020;