14-36205321-C-T

Variant names:

• chr14-36205321-C-T
• rs1952706
• ENST00000706910.1:n.64+11900G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000706910.1(PTCSC3):​n.64+11900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 151,078 control chromosomes in the GnomAD database, including 38,116 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 0.69 (38116 hom., cov: 28)
• Consequence: PTCSC3 ENST00000706910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

PTCSC3 (HGNC:43959): (papillary thyroid carcinoma susceptibility candidate 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000706910.1	n.64+11900G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.688 AC: 103892 AN: 150960 Hom.: 38104 Cov.: 28

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.688 AC: 103940 AN: 151078 Hom.: 38116 Cov.: 28 AF XY: 0.693 AC XY: 51074 AN XY: 73726

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.683

Alfa AF: 0.770 Hom.: 7448

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1952706; hg19: chr14-36674527;