rs10759944

chr9-97794690-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.777+9561T>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 0.725 in 151,986 control chromosomes in the GnomAD database, including 40,545 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 0.73 (40545 hom., cov: 30)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+9561T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+9561T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110130 AN: 151868 Hom.: 40511 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.725 AC: 110221 AN: 151986 Hom.: 40545 Cov.: 30 AF XY: 0.728 AC XY: 54100 AN XY: 74278

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.721

Alfa AF: 0.677 Hom.: 45089

Bravo AF: 0.734

Asia WGS AF: 0.802 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.11
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10759944; hg19: chr9-100556972;