ENST00000430058.2:n.331-11449G>A

Variant names:

• chr9-97734383-C-T
• rs7875482
• ENST00000430058.2:n.331-11449G>A

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.331-11449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,858 control chromosomes in the GnomAD database, including 11,289 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 0.38 (11289 hom., cov: 32)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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.778-9853G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.331-11449G>A		intron	N/A
	PTCSC2	ENST00000648027.1		n.471-9853G>A		intron	N/A
	PTCSC2	ENST00000648505.1		n.331-9853G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57093 AN: 151740 Hom.: 11269 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.376 AC: 57154 AN: 151858 Hom.: 11289 Cov.: 32 AF XY: 0.372 AC XY: 27623 AN XY: 74208

African (AFR) AF: 0.352 AC: 14588 AN: 41416

American (AMR) AF: 0.355 AC: 5415 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3468

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5178

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4810

European-Finnish (FIN) AF: 0.437 AC: 4600 AN: 10520

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28961 AN: 67894

Other (OTH) AF: 0.349 AC: 735 AN: 2106

Alfa AF: 0.399 Hom.: 5189

Bravo AF: 0.369

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs7875482; hg19: chr9-100496665;