dbSNP rs894673: PTCSC2:n.165+2928T>A (chr9-97849988-A-T) – 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+2928T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,112 control chromosomes in the GnomAD database, including 30,739 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 0.63 ( 30739 hom., cov: 32)

Consequence

PTCSC2
ENST00000649253.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.538

Publications

18 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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCSC2	NR_147055.1 link	n.165+2928T>A		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PTCSC2	ENST00000649253.2 link	n.165+2928T>A	intron_variant	Intron 1 of 5
PTCSC2	ENST00000649461.1 link	n.165+2928T>A	intron_variant	Intron 1 of 10
PTCSC2	ENST00000649526.1 link	n.165+2928T>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96197

AN:

151996

Hom.:

30712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.885

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.629

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

GnomAD4 genome

AF:

0.633

AC:

96261

AN:

152112

Hom.:

30739

Cov.:

AF XY:

0.637

AC XY:

47385

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.660

AC:

27390

AN:

41494

American (AMR)

AF:

0.652

AC:

9968

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1664

AN:

3472

East Asian (EAS)

AF:

0.886

AC:

4595

AN:

5186

South Asian (SAS)

AF:

0.633

AC:

3050

AN:

4820

European-Finnish (FIN)

AF:

0.640

AC:

6756

AN:

10556

Middle Eastern (MID)

AF:

0.616

AC:

180

AN:

292

European-Non Finnish (NFE)

AF:

0.603

AC:

40964

AN:

67978

Other (OTH)

AF:

0.628

AC:

1327

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1801

3602

5403

7204

9005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.620

Hom.:

3647

Bravo

AF:

0.637

Asia WGS

AF:

0.720

AC:

2507

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.54

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.

rs894673

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