rs944289

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 132 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC3	ENST00000706910.1		n.65-3644G>A		intron	N/A
	LINC00609	ENST00000818312.1		n.834+14196C>T		intron	N/A
	LINC00609	ENST00000818313.1		n.1244+14196C>T		intron	N/A

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

African (AFR) AF: 0.205 AC: 8518 AN: 41494

American (AMR) AF: 0.394 AC: 6020 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2312 AN: 5176

South Asian (SAS) AF: 0.499 AC: 2405 AN: 4822

European-Finnish (FIN) AF: 0.644 AC: 6784 AN: 10532

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39791 AN: 67976

Other (OTH) AF: 0.454 AC: 960 AN: 2116

Alfa AF: 0.544 Hom.: 107217

Bravo AF: 0.422

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.60
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs944289;

hg19: chr14-36649246;

COSMIC: COSV73615679;