chr9-97793827-A-G

Variant names:

• chr9-97793827-A-G
• rs965513
• ENST00000430058.2:n.330+12013T>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+12013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,126 control chromosomes in the GnomAD database, including 40,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Established risk allele (★).

• Frequency: Genomes: 𝑓 0.73 (40805 hom., cov: 31)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Established risk allele criteria provided, single submitter P:1
• Conservation: PhyloP100: -1.53
• Publications: 167 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=-0.97).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.777+10424T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.330+12013T>C		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+10424T>C		intron	N/A
	PTCSC2	ENST00000648505.1		n.330+12013T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110457 AN: 152008 Hom.: 40756 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.727 AC: 110565 AN: 152126 Hom.: 40805 Cov.: 31 AF XY: 0.730 AC XY: 54304 AN XY: 74366

African (AFR) AF: 0.838 AC: 34796 AN: 41506

American (AMR) AF: 0.713 AC: 10895 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2352 AN: 3472

East Asian (EAS) AF: 0.892 AC: 4610 AN: 5166

South Asian (SAS) AF: 0.772 AC: 3724 AN: 4824

European-Finnish (FIN) AF: 0.668 AC: 7063 AN: 10580

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44957 AN: 67978

Other (OTH) AF: 0.722 AC: 1524 AN: 2112

Alfa AF: 0.687 Hom.: 167541

Bravo AF: 0.736

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Established risk allele

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	-	Thyroid cancer, nonmedullary, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.79
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs965513; hg19: chr9-100556109;