chr9-97743548-C-A

Variant names:

• chr9-97743548-C-A
• rs2808699
• ENST00000562653.1:n.341C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562653.1(ENSG00000260677):​n.341C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,946 control chromosomes in the GnomAD database, including 10,634 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 0.36 (10634 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000260677 ENST00000562653.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 4 publications found

Genes affected

ENSG00000260677 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562653.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.778-19018G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260677	ENST00000562653.1	TSL:6	n.341C>A		non_coding_transcript_exon	Exon 1 of 1
	PTCSC2	ENST00000430058.2	TSL:2	n.331-20614G>T		intron	N/A
	PTCSC2	ENST00000648027.1		n.471-19018G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55041 AN: 151828 Hom.: 10622 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.340

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.363 AC: 55081 AN: 151946 Hom.: 10634 Cov.: 32 AF XY: 0.359 AC XY: 26633 AN XY: 74240

African (AFR) AF: 0.303 AC: 12563 AN: 41416

American (AMR) AF: 0.346 AC: 5278 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3472

East Asian (EAS) AF: 0.0474 AC: 246 AN: 5188

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4632 AN: 10520

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29023 AN: 67954

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.402 Hom.: 20918

Bravo AF: 0.352

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.52
PhyloP100		1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2808699;

hg19: chr9-100505830;