Genetic Variant ENST00000430058.2:n.330+11150T>C (chr9-97794690-A-G) – 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+11150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,986 control chromosomes in the GnomAD database, including 40,545 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 0.73 ( 40545 hom., cov: 30)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Publications

24 publications found

Variant links:

Genes affected

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

PTCSC2 links:

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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=-1.05).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.777+9561T>C		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.330+11150T>C	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.470+9561T>C	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.330+11150T>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.725

AC:

110130

AN:

151868

Hom.:

40511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.710

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.892

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.668

Gnomad MID

AF:

0.713

Gnomad NFE

AF:

0.663

Gnomad OTH

AF:

0.723

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

GnomAD4 genome

AF:

0.725

AC:

110221

AN:

151986

Hom.:

40545

Cov.:

AF XY:

0.728

AC XY:

54100

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.831

AC:

34488

AN:

41498

American (AMR)

AF:

0.710

AC:

10843

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2352

AN:

3468

East Asian (EAS)

AF:

0.892

AC:

4603

AN:

5160

South Asian (SAS)

AF:

0.771

AC:

3705

AN:

4806

European-Finnish (FIN)

AF:

0.668

AC:

7032

AN:

10524

Middle Eastern (MID)

AF:

0.712

AC:

208

AN:

292

European-Non Finnish (NFE)

AF:

0.663

AC:

45033

AN:

67954

Other (OTH)

AF:

0.721

AC:

1520

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1476

2952

4427

5903

7379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.682

Hom.:

58649

Bravo

AF:

0.734

Asia WGS

AF:

0.802

AC:

2792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.11

(source)

DANN

Benign

0.54

PhyloP100

-1.4

Splicing

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

Publications

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ENST00000430058.2:n.330+11150T>C

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