Genetic Variant PTCSC2:n.165+18207G>A (chr9-97834709-C-T) – 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+18207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,196 control chromosomes in the GnomAD database, including 1,859 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 0.11 ( 1859 hom., cov: 32)

Consequence

PTCSC2
ENST00000649253.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Publications

3 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.165+18207G>A		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.165+18207G>A	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.165+18207G>A	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.165+18207G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16709

AN:

152076

Hom.:

1848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.603

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.110

AC:

16730

AN:

152196

Hom.:

1859

Cov.:

AF XY:

0.116

AC XY:

8663

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0243

AC:

1011

AN:

41552

American (AMR)

AF:

0.185

AC:

2834

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0806

AC:

280

AN:

3472

East Asian (EAS)

AF:

0.604

AC:

3123

AN:

5170

South Asian (SAS)

AF:

0.125

AC:

602

AN:

4822

European-Finnish (FIN)

AF:

0.163

AC:

1719

AN:

10576

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6893

AN:

68006

Other (OTH)

AF:

0.105

AC:

221

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

668

1336

2004

2672

3340

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.132

Hom.:

1095

Bravo

AF:

0.110

Asia WGS

AF:

0.311

AC:

1079

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.93

(source)

DANN

Benign

0.17

PhyloP100

-1.2

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