ENST00000556013.4:n.426-6333C>T

Variant names:

• chr14-36169016-G-A
• rs934075
• ENST00000556013.4:n.426-6333C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556013.4(PTCSC3):​n.426-6333C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,804 control chromosomes in the GnomAD database, including 29,961 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 0.62 (29961 hom., cov: 30)
• Consequence: PTCSC3 ENST00000556013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 5 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 = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC3	NR_049735.3	n.426-6333C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000556013.4	n.426-6333C>T		intron_variant	Intron 1 of 3	1
PTCSC3	ENST00000706910.1	n.163+7282C>T		intron_variant	Intron 2 of 2
LINC00609	ENST00000818312.1	n.834+3172G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94328 AN: 151684 Hom.: 29937 Cov.: 30

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.654

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.622 AC: 94396 AN: 151804 Hom.: 29961 Cov.: 30 AF XY: 0.624 AC XY: 46281 AN XY: 74182

African (AFR) AF: 0.497 AC: 20541 AN: 41346

American (AMR) AF: 0.588 AC: 8971 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2434 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2582 AN: 5150

South Asian (SAS) AF: 0.620 AC: 2983 AN: 4808

European-Finnish (FIN) AF: 0.735 AC: 7748 AN: 10546

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46935 AN: 67932

Other (OTH) AF: 0.615 AC: 1292 AN: 2100

Alfa AF: 0.674 Hom.: 15977

Bravo AF: 0.600

Asia WGS AF: 0.576 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.26
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs934075; hg19: chr14-36638222;