rs934075

chr14-36169016-G-A

Variant summary

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

The NR_049735.2(PTCSC3):n.355-6333C>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 0.622 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 NR_049735.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

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=-0.91).
• 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/exons	MANE	UniProt
PTCSC3	NR_049735.2	n.355-6333C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC3	ENST00000556013.3	n.355-6333C>T		intron_variant, non_coding_transcript_variant		1
PTCSC3	ENST00000706910.1	n.163+7282C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.615

Alfa AF: 0.676 Hom.: 14112

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934075; hg19: chr14-36638222;