rs925488

chr9-97784109-G-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+20142C>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 0.717 in 152,056 control chromosomes in the GnomAD database, including 39,509 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 0.72 (39509 hom., cov: 31)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+20142C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+20142C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108893 AN: 151938 Hom.: 39484 Cov.: 31

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.717 AC: 108970 AN: 152056 Hom.: 39509 Cov.: 31 AF XY: 0.720 AC XY: 53541 AN XY: 74328

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.717

Alfa AF: 0.687 Hom.: 12432

Bravo AF: 0.724

Asia WGS AF: 0.801 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.16
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925488; hg19: chr9-100546391;