9-97820913-C-T

Variant names:

• chr9-97820913-C-T
• rs1443432
• ENST00000649253.2:n.166-10874G>A

Variant summary

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

The NR_147055.1(PTCSC2):​n.166-10874G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 151,970 control chromosomes in the GnomAD database, including 33,698 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 0.66 (33698 hom., cov: 31)
• Consequence: PTCSC2 NR_147055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_147055.1. 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.166-10874G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000649253.2		n.166-10874G>A		intron	N/A
	PTCSC2	ENST00000649461.1		n.166-10874G>A		intron	N/A
	PTCSC2	ENST00000649526.1		n.166-10874G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99856 AN: 151852 Hom.: 33665 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.658 AC: 99935 AN: 151970 Hom.: 33698 Cov.: 31 AF XY: 0.660 AC XY: 49021 AN XY: 74270

African (AFR) AF: 0.775 AC: 32132 AN: 41442

American (AMR) AF: 0.647 AC: 9892 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5101 AN: 5174

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6092 AN: 10538

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39477 AN: 67932

Other (OTH) AF: 0.661 AC: 1394 AN: 2108

Alfa AF: 0.627 Hom.: 47211

Bravo AF: 0.671

Asia WGS AF: 0.805 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.53
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1443432; hg19: chr9-100583195;