rs1877432

Positions:

• chr9-97781598-G-A

Variant summary

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

The NR_147055.1(PTCSC2):​n.777+22653C>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 0.359 in 151,864 control chromosomes in the GnomAD database, including 9,955 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 0.36 (9955 hom., cov: 31)
• Consequence: PTCSC2 NR_147055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.777+22653C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCSC2	ENST00000649461.1	n.777+22653C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54479 AN: 151746 Hom.: 9948 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.359 AC: 54500 AN: 151864 Hom.: 9955 Cov.: 31 AF XY: 0.354 AC XY: 26267 AN XY: 74196

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.399

Alfa AF: 0.385 Hom.: 23903

Bravo AF: 0.363

Asia WGS AF: 0.301 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1877432; hg19: chr9-100543880;