14-36140472-G-A

Variant names:

• chr14-36140472-G-A
• rs2415317
• ENST00000556013.4:n.577-4116C>T

Variant summary

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

The ENST00000556013.4(PTCSC3):​n.577-4116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,014 control chromosomes in the GnomAD database, including 18,088 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 0.46 (18088 hom., cov: 32)
• Consequence: PTCSC3 ENST00000556013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 10 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=-0.89).
• 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 rank	MANE	Protein	UniProt
PTCSC3	NR_049735.3	n.577-4116C>T		intron_variant	Intron 3 of 3
LINC00609	NR_073454.1	n.260-23648G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000556013.4	n.577-4116C>T		intron_variant	Intron 3 of 3	1
LINC00609	ENST00000546508.1	n.260-23648G>A		intron_variant	Intron 1 of 2	3
PTCSC3	ENST00000706908.1	n.317-4116C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69973 AN: 151896 Hom.: 18092 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.460 AC: 69973 AN: 152014 Hom.: 18088 Cov.: 32 AF XY: 0.463 AC XY: 34416 AN XY: 74312

African (AFR) AF: 0.223 AC: 9250 AN: 41476

American (AMR) AF: 0.404 AC: 6167 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3464

East Asian (EAS) AF: 0.444 AC: 2298 AN: 5178

South Asian (SAS) AF: 0.501 AC: 2409 AN: 4812

European-Finnish (FIN) AF: 0.643 AC: 6781 AN: 10544

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39837 AN: 67946

Other (OTH) AF: 0.460 AC: 972 AN: 2112

Alfa AF: 0.533 Hom.: 61283

Bravo AF: 0.430

Asia WGS AF: 0.443 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.87
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2415317; hg19: chr14-36609678;