ENST00000430058.2:n.331-11706C>T

Variant names:

• chr9-97734640-G-A
• rs2805809
• ENST00000430058.2:n.331-11706C>T

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.331-11706C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,088 control chromosomes in the GnomAD database, including 11,394 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 0.38 (11394 hom., cov: 32)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430058.2. 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.778-10110C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.331-11706C>T		intron	N/A
	PTCSC2	ENST00000648027.1		n.471-10110C>T		intron	N/A
	PTCSC2	ENST00000648505.1		n.331-10110C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57304 AN: 151970 Hom.: 11374 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.377 AC: 57365 AN: 152088 Hom.: 11394 Cov.: 32 AF XY: 0.373 AC XY: 27765 AN XY: 74368

African (AFR) AF: 0.353 AC: 14654 AN: 41478

American (AMR) AF: 0.355 AC: 5418 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3464

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5182

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4654 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29032 AN: 67972

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.397 Hom.: 2127

Bravo AF: 0.369

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.56
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2805809; hg19: chr9-100496922;