rs944289

Variant names:

• chr14-36180040-C-T
• rs944289
• ENST00000706910.1:n.65-3644G>A

Variant summary

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

The ENST00000706910.1(PTCSC3):​n.65-3644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,048 control chromosomes in the GnomAD database, including 17,831 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 0.45 (17831 hom., cov: 33)
• Consequence: PTCSC3 ENST00000706910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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.65-3644G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68989 AN: 151930 Hom.: 17832 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.454 AC: 68990 AN: 152048 Hom.: 17831 Cov.: 33 AF XY: 0.457 AC XY: 33977 AN XY: 74326

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.454

Alfa AF: 0.559 Hom.: 55239

Bravo AF: 0.422

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs944289; hg19: chr14-36649246; COSMIC: COSV73615679;