rs10217225

Variant names:

• chr9-97834709-C-T
• rs10217225
• ENST00000649253.2:n.165+18207G>A

Variant summary

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

The NR_147055.1(PTCSC2):​n.165+18207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,196 control chromosomes in the GnomAD database, including 1,859 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 0.11 (1859 hom., cov: 32)
• Consequence: PTCSC2 NR_147055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147055.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.165+18207G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000649253.2		n.165+18207G>A		intron	N/A
	PTCSC2	ENST00000649461.1		n.165+18207G>A		intron	N/A
	PTCSC2	ENST00000649526.1		n.165+18207G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16709 AN: 152076 Hom.: 1848 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.110 AC: 16730 AN: 152196 Hom.: 1859 Cov.: 32 AF XY: 0.116 AC XY: 8663 AN XY: 74402

African (AFR) AF: 0.0243 AC: 1011 AN: 41552

American (AMR) AF: 0.185 AC: 2834 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3123 AN: 5170

South Asian (SAS) AF: 0.125 AC: 602 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1719 AN: 10576

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6893 AN: 68006

Other (OTH) AF: 0.105 AC: 221 AN: 2104

Alfa AF: 0.132 Hom.: 1095

Bravo AF: 0.110

Asia WGS AF: 0.311 AC: 1079 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.17
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10217225; hg19: chr9-100596991;