ENST00000649253.2:n.166-10753A>G

Variant names:

• chr9-97820792-T-C
• rs10124220
• ENST00000649253.2:n.166-10753A>G

Variant summary

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

The ENST00000649253.2(PTCSC2):​n.166-10753A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,088 control chromosomes in the GnomAD database, including 34,780 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 0.67 (34780 hom., cov: 32)
• Consequence: PTCSC2 ENST00000649253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649253.2. 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.166-10753A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000649253.2		n.166-10753A>G		intron	N/A
	PTCSC2	ENST00000649461.1		n.166-10753A>G		intron	N/A
	PTCSC2	ENST00000649526.1		n.166-10753A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101655 AN: 151970 Hom.: 34748 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.669 AC: 101733 AN: 152088 Hom.: 34780 Cov.: 32 AF XY: 0.672 AC XY: 49955 AN XY: 74340

African (AFR) AF: 0.778 AC: 32251 AN: 41480

American (AMR) AF: 0.650 AC: 9936 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3466

East Asian (EAS) AF: 0.986 AC: 5112 AN: 5184

South Asian (SAS) AF: 0.683 AC: 3290 AN: 4820

European-Finnish (FIN) AF: 0.616 AC: 6510 AN: 10564

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

European-Non Finnish (NFE) AF: 0.597 AC: 40610 AN: 67970

Other (OTH) AF: 0.666 AC: 1410 AN: 2116

Alfa AF: 0.647 Hom.: 6465

Bravo AF: 0.679

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.52
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10124220; hg19: chr9-100583074;