dbSNP rs12352658: PTCSC2:n.330+16354C>T (chr9-97789486-G-A) – 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+16354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,946 control chromosomes in the GnomAD database, including 9,457 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 0.34 ( 9457 hom., cov: 32)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

5 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.777+14765C>T		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.330+16354C>T	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.470+14765C>T	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.330+16354C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.343

AC:

52070

AN:

151828

Hom.:

9442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.427

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.311

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

GnomAD4 genome

AF:

0.343

AC:

52115

AN:

151946

Hom.:

9457

Cov.:

AF XY:

0.350

AC XY:

25970

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.427

AC:

17698

AN:

41432

American (AMR)

AF:

0.333

AC:

5082

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

932

AN:

3468

East Asian (EAS)

AF:

0.520

AC:

2678

AN:

5154

South Asian (SAS)

AF:

0.466

AC:

2249

AN:

4822

European-Finnish (FIN)

AF:

0.360

AC:

3789

AN:

10538

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.275

AC:

18686

AN:

67946

Other (OTH)

AF:

0.310

AC:

655

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1732

3464

5195

6927

8659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.273

Hom.:

2154

Bravo

AF:

0.341

Asia WGS

AF:

0.473

AC:

1644

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

9.5

(source)

DANN

Benign

0.82

PhyloP100

0.35

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