rs10759944

Variant names:

• chr9-97794690-A-G
• rs10759944
• ENST00000430058.2:n.330+11150T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430058.2(PTCSC2):​n.330+11150T>C variant causes a intron 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 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430058.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.777+9561T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.330+11150T>C		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+9561T>C		intron	N/A
	PTCSC2	ENST00000648505.1		n.330+11150T>C		intron	N/A

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

African (AFR) AF: 0.831 AC: 34488 AN: 41498

American (AMR) AF: 0.710 AC: 10843 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4603 AN: 5160

South Asian (SAS) AF: 0.771 AC: 3705 AN: 4806

European-Finnish (FIN) AF: 0.668 AC: 7032 AN: 10524

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.663 AC: 45033 AN: 67954

Other (OTH) AF: 0.721 AC: 1520 AN: 2108

Alfa AF: 0.682 Hom.: 58649

Bravo AF: 0.734

Asia WGS AF: 0.802 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10759944;

hg19: chr9-100556972;