14-36205321-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

LINC00609 (HGNC:43960): (long intergenic non-protein coding RNA 609)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706910.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC3	ENST00000706910.1		n.64+11900G>A		intron	N/A
	LINC00609	ENST00000818312.1		n.835-30003C>T		intron	N/A
	LINC00609	ENST00000818313.1		n.1245-9638C>T		intron	N/A

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

African (AFR) AF: 0.437 AC: 17965 AN: 41094

American (AMR) AF: 0.631 AC: 9540 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2660 AN: 3462

East Asian (EAS) AF: 0.590 AC: 2981 AN: 5052

South Asian (SAS) AF: 0.752 AC: 3589 AN: 4772

European-Finnish (FIN) AF: 0.891 AC: 9378 AN: 10522

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.818 AC: 55427 AN: 67784

Other (OTH) AF: 0.683 AC: 1421 AN: 2082

Alfa AF: 0.747 Hom.: 14494

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.48
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1952706; hg19: chr14-36674527;