rs7847449

chr9-97789626-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147055.1(PTCSC2):n.777+14625G>T 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 0.307 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 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+14625G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+14625G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.330

Alfa AF: 0.318 Hom.: 2488

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7847449; hg19: chr9-100551908;