9-97852835-C-T

Variant names:

• chr9-97852835-C-T
• rs907577
• ENST00000649253.2:n.165+81G>A

Variant summary

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

The ENST00000649253.2(PTCSC2):​n.165+81G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,146 control chromosomes in the GnomAD database, including 30,815 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 0.63 (30815 hom., cov: 33)
• Consequence: PTCSC2 ENST00000649253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1	n.165+81G>A		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC2	ENST00000649253.2	n.165+81G>A		intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1	n.165+81G>A		intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1	n.165+81G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96295 AN: 152030 Hom.: 30788 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.633 AC: 96358 AN: 152146 Hom.: 30815 Cov.: 33 AF XY: 0.638 AC XY: 47435 AN XY: 74378

African (AFR) AF: 0.662 AC: 27497 AN: 41522

American (AMR) AF: 0.651 AC: 9959 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4570 AN: 5154

South Asian (SAS) AF: 0.633 AC: 3057 AN: 4832

European-Finnish (FIN) AF: 0.640 AC: 6773 AN: 10580

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40962 AN: 67982

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.618 Hom.: 4240

Bravo AF: 0.637

Asia WGS AF: 0.720 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.81
PhyloP100		-0.79
PromoterAI		-0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs907577; hg19: chr9-100615117;