rs7847449

Variant names:

• chr9-97789626-C-A
• rs7847449
• ENST00000430058.2:n.330+16214G>T

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+16214G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,970 control chromosomes in the GnomAD database, including 7,416 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 0.31 (7416 hom., cov: 31)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.777+14625G>T		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000430058.2	n.330+16214G>T		intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1	n.470+14625G>T		intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1	n.330+16214G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46578 AN: 151852 Hom.: 7404 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.307 AC: 46611 AN: 151970 Hom.: 7416 Cov.: 31 AF XY: 0.303 AC XY: 22460 AN XY: 74242

African (AFR) AF: 0.262 AC: 10869 AN: 41428

American (AMR) AF: 0.264 AC: 4037 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5160

South Asian (SAS) AF: 0.249 AC: 1195 AN: 4808

European-Finnish (FIN) AF: 0.288 AC: 3048 AN: 10566

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24319 AN: 67940

Other (OTH) AF: 0.330 AC: 696 AN: 2106

Alfa AF: 0.324 Hom.: 3972

Bravo AF: 0.306

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7847449; hg19: chr9-100551908;