Genetic Variant PTCSC2:n.330+30320T>G (chr9-97775520-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430058.2(PTCSC2):n.330+30320T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,058 control chromosomes in the GnomAD database, including 39,644 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 0.72 ( 39644 hom., cov: 32)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.879

Publications

20 publications found

Variant links:

Genes affected

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

PTCSC2 links:

Genome browser will be placed here

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.777+28731T>G		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.330+30320T>G	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.470+28731T>G	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.330+30320T>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109056

AN:

151940

Hom.:

39611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.805

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.889

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.720

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

GnomAD4 genome

AF:

0.718

AC:

109144

AN:

152058

Hom.:

39644

Cov.:

AF XY:

0.721

AC XY:

53600

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.805

AC:

33401

AN:

41476

American (AMR)

AF:

0.708

AC:

10821

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2353

AN:

3472

East Asian (EAS)

AF:

0.890

AC:

4606

AN:

5176

South Asian (SAS)

AF:

0.772

AC:

3708

AN:

4806

European-Finnish (FIN)

AF:

0.670

AC:

7065

AN:

10552

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.662

AC:

45029

AN:

67980

Other (OTH)

AF:

0.718

AC:

1516

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1554

3109

4663

6218

7772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.669

Hom.:

6609

Bravo

AF:

0.725

Asia WGS

AF:

0.802

AC:

2789

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.5

(source)

DANN

Benign

0.75

PhyloP100

-0.88

Splicing

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

Publications

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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