rs7030241

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_147055.1(PTCSC2):​n.777+16158A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,004 control chromosomes in the GnomAD database, including 39,826 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 0.72 ( 39826 hom., cov: 30)

Consequence

PTCSC2
NR_147055.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
Variant links:
Genes affected
PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTCSC2NR_147055.1 linkuse as main transcriptn.777+16158A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTCSC2ENST00000649461.1 linkuse as main transcriptn.777+16158A>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.719
AC:
109277
AN:
151886
Hom.:
39799
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.812
Gnomad AMI
AF:
0.479
Gnomad AMR
AF:
0.709
Gnomad ASJ
AF:
0.678
Gnomad EAS
AF:
0.891
Gnomad SAS
AF:
0.773
Gnomad FIN
AF:
0.669
Gnomad MID
AF:
0.718
Gnomad NFE
AF:
0.662
Gnomad OTH
AF:
0.720
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.719
AC:
109357
AN:
152004
Hom.:
39826
Cov.:
30
AF XY:
0.723
AC XY:
53723
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.812
Gnomad4 AMR
AF:
0.709
Gnomad4 ASJ
AF:
0.678
Gnomad4 EAS
AF:
0.891
Gnomad4 SAS
AF:
0.772
Gnomad4 FIN
AF:
0.669
Gnomad4 NFE
AF:
0.662
Gnomad4 OTH
AF:
0.718
Alfa
AF:
0.591
Hom.:
1777
Bravo
AF:
0.727
Asia WGS
AF:
0.803
AC:
2793
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.1
DANN
Benign
0.30

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7030241; hg19: chr9-100550375; API