rs2787417

Variant names:

• chr14-36182597-T-C
• rs2787417
• ENST00000706910.1:n.65-6201A>G

Variant summary

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

The ENST00000706910.1(PTCSC3):​n.65-6201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,784 control chromosomes in the GnomAD database, including 33,336 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 0.66 (33336 hom., cov: 32)
• Consequence: PTCSC3 ENST00000706910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCSC3	ENST00000706910.1	n.65-6201A>G		intron_variant	Intron 1 of 2
LINC00609	ENST00000818312.1	n.834+16753T>C		intron_variant	Intron 6 of 6
LINC00609	ENST00000818313.1	n.1244+16753T>C		intron_variant	Intron 7 of 9
LINC00609	ENST00000818317.1	n.879-11939T>C		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99458 AN: 151670 Hom.: 33314 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.656 AC: 99515 AN: 151784 Hom.: 33336 Cov.: 32 AF XY: 0.658 AC XY: 48828 AN XY: 74168

African (AFR) AF: 0.537 AC: 22207 AN: 41376

American (AMR) AF: 0.608 AC: 9276 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2653 AN: 5134

South Asian (SAS) AF: 0.616 AC: 2963 AN: 4812

European-Finnish (FIN) AF: 0.805 AC: 8418 AN: 10454

Middle Eastern (MID) AF: 0.662 AC: 192 AN: 290

European-Non Finnish (NFE) AF: 0.725 AC: 49257 AN: 67962

Other (OTH) AF: 0.645 AC: 1361 AN: 2110

Alfa AF: 0.701 Hom.: 4767

Bravo AF: 0.632

Asia WGS AF: 0.580 AC: 2018 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.36
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2787417; hg19: chr14-36651803;