rs2415317

Positions:

• chr14-36140472-G-A
• chr14-36140472-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_049735.2(PTCSC3):​n.506-4116C>T variant causes a intron, non coding transcript 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 NR_049735.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PTCSC3	NR_049735.2	n.506-4116C>T		intron_variant, non_coding_transcript_variant
LINC00609	NR_073454.1	n.260-23648G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00609	ENST00000546508.1	n.260-23648G>A		intron_variant, non_coding_transcript_variant		3
PTCSC3	ENST00000706910.1	n.164-4116C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.460

Alfa AF: 0.558 Hom.: 38638

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2415317; hg19: chr14-36609678;