chr9-97795009-C-T

Variant names:

• chr9-97795009-C-T
• rs16924274
• ENST00000430058.2:n.330+10831G>A

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+10831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,824 control chromosomes in the GnomAD database, including 5,731 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 0.26 (5731 hom., cov: 31)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.777+9242G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.330+10831G>A		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+9242G>A		intron	N/A
	PTCSC2	ENST00000648505.1		n.330+10831G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40098 AN: 151706 Hom.: 5723 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.264 AC: 40131 AN: 151824 Hom.: 5731 Cov.: 31 AF XY: 0.272 AC XY: 20158 AN XY: 74192

African (AFR) AF: 0.280 AC: 11569 AN: 41358

American (AMR) AF: 0.287 AC: 4384 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3460

East Asian (EAS) AF: 0.511 AC: 2635 AN: 5156

South Asian (SAS) AF: 0.455 AC: 2179 AN: 4790

European-Finnish (FIN) AF: 0.291 AC: 3068 AN: 10532

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14872 AN: 67944

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.230 Hom.: 10266

Bravo AF: 0.260

Asia WGS AF: 0.451 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs16924274; hg19: chr9-100557291;