14-36205321-C-T

Position:

• chr14-36205321-C-T

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000706910.1	n.64+11900G>A		intron_variant, non_coding_transcript_variant

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;