Genetic Variant PTCSC2:n.166-10753A>G (chr9-97820792-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 NR_147055.1(PTCSC2):n.166-10753A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,088 control chromosomes in the GnomAD database, including 34,780 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 0.67 ( 34780 hom., cov: 32)

Consequence

PTCSC2
NR_147055.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.891

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.166-10753A>G		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.166-10753A>G	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.166-10753A>G	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.166-10753A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101655

AN:

151970

Hom.:

34748

Cov.:

show subpopulations

Gnomad AFR

AF:

0.778

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.986

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.616

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.668

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

GnomAD4 genome

AF:

0.669

AC:

101733

AN:

152088

Hom.:

34780

Cov.:

AF XY:

0.672

AC XY:

49955

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.778

AC:

32251

AN:

41480

American (AMR)

AF:

0.650

AC:

9936

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.601

AC:

2083

AN:

3466

East Asian (EAS)

AF:

0.986

AC:

5112

AN:

5184

South Asian (SAS)

AF:

0.683

AC:

3290

AN:

4820

European-Finnish (FIN)

AF:

0.616

AC:

6510

AN:

10564

Middle Eastern (MID)

AF:

0.639

AC:

188

AN:

294

European-Non Finnish (NFE)

AF:

0.597

AC:

40610

AN:

67970

Other (OTH)

AF:

0.666

AC:

1410

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1698

3395

5093

6790

8488

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.647

Hom.:

6465

Bravo

AF:

0.679

Asia WGS

AF:

0.806

AC:

2805

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.86

(source)

DANN

Benign

0.52

PhyloP100

-0.89

Splicing

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

Publications

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9-97820792-T-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