Genetic Variant PTCSC2:n.330+10831G>A (chr9-97795009-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 ENST00000430058.2(PTCSC2):n.330+10831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,824 control chromosomes in the GnomAD database, including 5,731 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 0.26 ( 5731 hom., cov: 31)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.543

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.777+9242G>A		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.330+10831G>A	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.470+9242G>A	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.330+10831G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40098

AN:

151706

Hom.:

5723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.264

AC:

40131

AN:

151824

Hom.:

5731

Cov.:

AF XY:

0.272

AC XY:

20158

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.280

AC:

11569

AN:

41358

American (AMR)

AF:

0.287

AC:

4384

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

699

AN:

3460

East Asian (EAS)

AF:

0.511

AC:

2635

AN:

5156

South Asian (SAS)

AF:

0.455

AC:

2179

AN:

4790

European-Finnish (FIN)

AF:

0.291

AC:

3068

AN:

10532

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14872

AN:

67944

Other (OTH)

AF:

0.243

AC:

512

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1478

2955

4433

5910

7388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.230

Hom.:

10266

Bravo

AF:

0.260

Asia WGS

AF:

0.451

AC:

1566

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.4

(source)

DANN

Benign

0.79

PhyloP100

0.54

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