9-97716232-T-C

Position:

• chr9-97716232-T-C

Variant summary

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

The NR_147055.1(PTCSC2):​n.1295+1417A>G 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 0.369 in 150,760 control chromosomes in the GnomAD database, including 10,289 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 0.37 (10289 hom., cov: 29)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.1295+1417A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.1295+1417A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55619 AN: 150642 Hom.: 10275 Cov.: 29

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.369 AC: 55683 AN: 150760 Hom.: 10289 Cov.: 29 AF XY: 0.370 AC XY: 27228 AN XY: 73560

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.378

Alfa AF: 0.337 Hom.: 1083

Bravo AF: 0.370

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2808680; hg19: chr9-100478514;