Variant 9-97845777-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_147055.1(PTCSC2):n.165+7139G>C 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 0.179 in 152,016 control chromosomes in the GnomAD database, including 2,789 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 0.18 ( 2789 hom., cov: 31)

Consequence

PTCSC2
NR_147055.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170

Variant links:

Genes affected

PTCSC2 (HGNC:44086): (papillary thyroid carcinoma susceptibility candidate 2)

PTCSC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1 linkuse as main transcript	n.165+7139G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect
PTCSC2	ENST00000649461.1 linkuse as main transcript	n.165+7139G>C	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000649526.1 linkuse as main transcript	n.165+7139G>C	intron_variant, non_coding_transcript_variant
PTCSC2	ENST00000650104.1 linkuse as main transcript	n.165+7139G>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27118

AN:

151898

Hom.:

2778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.0437

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.186

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

GnomAD4 genome

AF:

0.179

AC:

27165

AN:

152016

Hom.:

2789

Cov.:

AF XY:

0.180

AC XY:

13403

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.283

Gnomad4 EAS

AF:

0.0438

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.191

Gnomad4 NFE

AF:

0.128

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.153

Hom.:

247

Bravo

AF:

0.183

Asia WGS

AF:

0.169

AC:

585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.5

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over