chr14-36180040-C-T

Position:

• chr14-36180040-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000706910.1	n.65-3644G>A		intron_variant, non_coding_transcript_variant

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;