Genetic Variant PTCSC2:n.1295+1417A>G (chr9-97716232-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000649461.1(PTCSC2):n.1295+1417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 150,760 control chromosomes in the GnomAD database, including 10,289 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 0.37 ( 10289 hom., cov: 29)

Consequence

PTCSC2
ENST00000649461.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.284

Publications

3 publications found

Variant links:

Genes affected

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

PTCSC2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.1295+1417A>G		intron_variant	Intron 8 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649461.1 link	n.1295+1417A>G	intron_variant	Intron 8 of 10
PTCSC2	ENST00000824737.1 link	n.600-2425A>G	intron_variant	Intron 4 of 6
PTCSC2	ENST00000824738.1 link	n.886+1417A>G	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

55619

AN:

150642

Hom.:

10275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.361

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.375

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

GnomAD4 genome

AF:

0.369

AC:

55683

AN:

150760

Hom.:

10289

Cov.:

AF XY:

0.370

AC XY:

27228

AN XY:

73560

show subpopulations

African (AFR)

AF:

0.405

AC:

16632

AN:

41020

American (AMR)

AF:

0.346

AC:

5224

AN:

15118

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

1346

AN:

3466

East Asian (EAS)

AF:

0.351

AC:

1784

AN:

5076

South Asian (SAS)

AF:

0.362

AC:

1731

AN:

4782

European-Finnish (FIN)

AF:

0.365

AC:

3744

AN:

10246

Middle Eastern (MID)

AF:

0.517

AC:

150

AN:

290

European-Non Finnish (NFE)

AF:

0.353

AC:

23912

AN:

67770

Other (OTH)

AF:

0.378

AC:

790

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1767

3533

5300

7066

8833

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.337

Hom.:

1083

Bravo

AF:

0.370

Asia WGS

AF:

0.355

AC:

1231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.8

(source)

DANN

Benign

0.50

PhyloP100

0.28

Splicing

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

Publications

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9-97716232-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over