9-97786652-C-T

Variant names:

• chr9-97786652-C-T
• rs7864322
• ENST00000824829.1:n.18C>T

Variant summary

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

The ENST00000824829.1(ENSG00000307267):​n.18C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,048 control chromosomes in the GnomAD database, including 39,829 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 (39829 hom., cov: 31)
• Consequence: ENSG00000307267 ENST00000824829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 8 publications found

Genes affected

ENSG00000307267 (HGNC:):

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824829.1. 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.777+17599G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307267	ENST00000824829.1		n.18C>T		non_coding_transcript_exon	Exon 1 of 2
	PTCSC2	ENST00000430058.2	TSL:2	n.330+19188G>A		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+17599G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109304 AN: 151930 Hom.: 39802 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.719 AC: 109384 AN: 152048 Hom.: 39829 Cov.: 31 AF XY: 0.723 AC XY: 53745 AN XY: 74324

African (AFR) AF: 0.812 AC: 33663 AN: 41482

American (AMR) AF: 0.709 AC: 10832 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4611 AN: 5180

South Asian (SAS) AF: 0.773 AC: 3722 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7061 AN: 10550

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44978 AN: 67952

Other (OTH) AF: 0.718 AC: 1516 AN: 2110

Alfa AF: 0.696 Hom.: 7411

Bravo AF: 0.727

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7864322; hg19: chr9-100548934;