Genetic Variant PTCSC2:n.165+19033A>G (chr9-97833883-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 ENST00000649253.2(PTCSC2):n.165+19033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,264 control chromosomes in the GnomAD database, including 1,321 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 0.12 ( 1321 hom., cov: 33)

Consequence

PTCSC2
ENST00000649253.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

4 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.165+19033A>G		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.165+19033A>G	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.165+19033A>G	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.165+19033A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18967

AN:

152146

Hom.:

1313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.00771

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.126

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

GnomAD4 genome

AF:

0.125

AC:

19008

AN:

152264

Hom.:

1321

Cov.:

AF XY:

0.128

AC XY:

9498

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.160

AC:

6639

AN:

41566

American (AMR)

AF:

0.134

AC:

2055

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

445

AN:

3468

East Asian (EAS)

AF:

0.00792

AC:

AN:

5176

South Asian (SAS)

AF:

0.112

AC:

543

AN:

4834

European-Finnish (FIN)

AF:

0.184

AC:

1947

AN:

10586

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6895

AN:

68014

Other (OTH)

AF:

0.129

AC:

273

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

878

1755

2633

3510

4388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.111

Hom.:

1709

Bravo

AF:

0.123

Asia WGS

AF:

0.105

AC:

365

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.7

(source)

DANN

Benign

0.56

PhyloP100

-0.054

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