dbSNP rs2805809: PTCSC2:n.331-11706C>T (chr9-97734640-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000430058.2(PTCSC2):n.331-11706C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,088 control chromosomes in the GnomAD database, including 11,394 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 0.38 ( 11394 hom., cov: 32)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Variant links:

Genes affected

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

PTCSC2 links:

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ACMG classification

Classification made for transcript

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 = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.778-10110C>T		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.331-11706C>T	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.471-10110C>T	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.331-10110C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57304

AN:

151970

Hom.:

11374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.0466

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.440

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.377

AC:

57365

AN:

152088

Hom.:

11394

Cov.:

AF XY:

0.373

AC XY:

27765

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.290

Gnomad4 EAS

AF:

0.0465

Gnomad4 SAS

AF:

0.263

Gnomad4 FIN

AF:

0.440

Gnomad4 NFE

AF:

0.427

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.399

Hom.:

2084

Bravo

AF:

0.369

Asia WGS

AF:

0.190

AC:

661

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

6.6

DANN

Benign

0.56

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over