dbSNP rs7048394: PTCSC2:n.165+9765A>G (chr9-97843151-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+9765A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,222 control chromosomes in the GnomAD database, including 51,401 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 0.82 ( 51401 hom., cov: 32)

Consequence

PTCSC2
ENST00000649253.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Publications

9 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.165+9765A>G		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.165+9765A>G	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.165+9765A>G	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.165+9765A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

124085

AN:

152104

Hom.:

51344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.940

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.820

Gnomad ASJ

AF:

0.764

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.831

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.819

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

GnomAD4 genome

AF:

0.816

AC:

124195

AN:

152222

Hom.:

51401

Cov.:

AF XY:

0.823

AC XY:

61226

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.940

AC:

39069

AN:

41554

American (AMR)

AF:

0.820

AC:

12547

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.764

AC:

2648

AN:

3468

East Asian (EAS)

AF:

0.994

AC:

5146

AN:

5178

South Asian (SAS)

AF:

0.800

AC:

3846

AN:

4810

European-Finnish (FIN)

AF:

0.831

AC:

8803

AN:

10598

Middle Eastern (MID)

AF:

0.816

AC:

240

AN:

294

European-Non Finnish (NFE)

AF:

0.730

AC:

49634

AN:

68002

Other (OTH)

AF:

0.821

AC:

1734

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1127

2254

3380

4507

5634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<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:

0.779

Hom.:

6057

Bravo

AF:

0.824

Asia WGS

AF:

0.915

AC:

3185

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.29

(source)

DANN

Benign

0.74

PhyloP100

-1.6

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