chr9-97775520-A-C

Variant names:

• chr9-97775520-A-C
• rs1588635
• ENST00000430058.2:n.330+30320T>G

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.330+30320T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,058 control chromosomes in the GnomAD database, including 39,644 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 (39644 hom., cov: 32)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• Publications: 20 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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+28731T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.330+30320T>G		intron	N/A
	PTCSC2	ENST00000648027.1		n.470+28731T>G		intron	N/A
	PTCSC2	ENST00000648505.1		n.330+30320T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109056 AN: 151940 Hom.: 39611 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.670

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: 0.718 AC: 109144 AN: 152058 Hom.: 39644 Cov.: 32 AF XY: 0.721 AC XY: 53600 AN XY: 74308

African (AFR) AF: 0.805 AC: 33401 AN: 41476

American (AMR) AF: 0.708 AC: 10821 AN: 15286

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

East Asian (EAS) AF: 0.890 AC: 4606 AN: 5176

South Asian (SAS) AF: 0.772 AC: 3708 AN: 4806

European-Finnish (FIN) AF: 0.670 AC: 7065 AN: 10552

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

European-Non Finnish (NFE) AF: 0.662 AC: 45029 AN: 67980

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

Alfa AF: 0.669 Hom.: 6609

Bravo AF: 0.725

Asia WGS AF: 0.802 AC: 2789 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.88

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: rs1588635;

hg19: chr9-100537802;