ENST00000430058.2:n.331-26115G>A

Variant names:

• chr9-97749049-C-T
• rs16924016
• ENST00000430058.2:n.331-26115G>A

Variant summary

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

The ENST00000430058.2(PTCSC2):​n.331-26115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,186 control chromosomes in the GnomAD database, including 637 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 0.084 (637 hom., cov: 32)
• Consequence: PTCSC2 ENST00000430058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 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 = 0.196 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.778-24519G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	ENST00000430058.2	TSL:2	n.331-26115G>A		intron	N/A
	PTCSC2	ENST00000648027.1		n.471-24519G>A		intron	N/A
	PTCSC2	ENST00000648505.1		n.331-24519G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12754 AN: 152068 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0853

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0838 AC: 12754 AN: 152186 Hom.: 637 Cov.: 32 AF XY: 0.0850 AC XY: 6325 AN XY: 74408

African (AFR) AF: 0.0967 AC: 4016 AN: 41512

American (AMR) AF: 0.103 AC: 1577 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5170

South Asian (SAS) AF: 0.0702 AC: 338 AN: 4814

European-Finnish (FIN) AF: 0.0853 AC: 904 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0606 AC: 4124 AN: 68008

Other (OTH) AF: 0.0956 AC: 202 AN: 2112

Alfa AF: 0.0735 Hom.: 1602

Bravo AF: 0.0864

Asia WGS AF: 0.131 AC: 457 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	0.010
DANN	Benign	0.78
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs16924016; hg19: chr9-100511331;