dbSNP rs2808693: PTCSC2:n.331-5542T>C (chr9-97728476-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.331-5542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,056 control chromosomes in the GnomAD database, including 14,223 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 0.42 ( 14223 hom., cov: 32)

Consequence

PTCSC2
ENST00000430058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.778-3946T>C		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PTCSC2	ENST00000430058.2 link	n.331-5542T>C	intron_variant	Intron 2 of 2	2
PTCSC2	ENST00000648027.1 link	n.471-3946T>C	intron_variant	Intron 3 of 4
PTCSC2	ENST00000648505.1 link	n.331-3946T>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63954

AN:

151938

Hom.:

14201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.505

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.0466

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.440

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.381

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

GnomAD4 genome

AF:

0.421

AC:

64022

AN:

152056

Hom.:

14223

Cov.:

AF XY:

0.415

AC XY:

30861

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.505

AC:

20948

AN:

41458

American (AMR)

AF:

0.373

AC:

5694

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

985

AN:

3468

East Asian (EAS)

AF:

0.0465

AC:

241

AN:

5182

South Asian (SAS)

AF:

0.264

AC:

1275

AN:

4824

European-Finnish (FIN)

AF:

0.440

AC:

4655

AN:

10572

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.428

AC:

29060

AN:

67954

Other (OTH)

AF:

0.381

AC:

806

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1854

3708

5563

7417

9271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<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:

0.426

Hom.:

2454

Bravo

AF:

0.420

Asia WGS

AF:

0.196

AC:

682

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.1

(source)

DANN

Benign

0.66

PhyloP100

-0.044

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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