rs2808693

chr9-97728476-A-G

Variant summary

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

The NR_147055.1(PTCSC2):n.778-3946T>C 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 0.421 in 152,056 control chromosomes in the GnomAD database, including 14,223 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 0.42 (14223 hom., cov: 32)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.778-3946T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.778-3946T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63954 AN: 151938 Hom.: 14201 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.421 AC: 64022 AN: 152056 Hom.: 14223 Cov.: 32 AF XY: 0.415 AC XY: 30861 AN XY: 74312

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.381

Alfa AF: 0.424 Hom.: 2360

Bravo AF: 0.420

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808693; hg19: chr9-100490758;