ENST00000400056.3:n.683T>C

Variant names:

• chr9-97700127-T-C
• rs10817938
• ENST00000400056.3:n.683T>C

Variant summary

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

The ENST00000400056.3(KRT18P13):​n.683T>C 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 0.0413 in 609,994 control chromosomes in the GnomAD database, including 1,048 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 0.036 (218 hom., cov: 32)
  • Exomes 𝑓: 0.043 (830 hom.)
• Consequence: KRT18P13 ENST00000400056.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 17 publications found

Genes affected

KRT18P13 (HGNC:6432): (keratin 18 pseudogene 13)

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400056.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCSC2	NR_147055.1		n.1501-56A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT18P13	ENST00000400056.3	TSL:6	n.683T>C		non_coding_transcript_exon	Exon 2 of 2
	PTCSC2	ENST00000649461.1		n.1501-56A>G		intron	N/A
	PTCSC2	ENST00000824737.1		n.805-56A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5456 AN: 152182 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.00794

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.00668

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0431 AC: 19720 AN: 457694 Hom.: 830 Cov.: 0 AF XY: 0.0433 AC XY: 10929 AN XY: 252158

African (AFR) AF: 0.00797 AC: 98 AN: 12292

American (AMR) AF: 0.0718 AC: 2130 AN: 29648

Ashkenazi Jewish (ASJ) AF: 0.0310 AC: 426 AN: 13720

East Asian (EAS) AF: 0.206 AC: 4719 AN: 22948

South Asian (SAS) AF: 0.0515 AC: 2887 AN: 56092

European-Finnish (FIN) AF: 0.00480 AC: 133 AN: 27700

Middle Eastern (MID) AF: 0.0833 AC: 146 AN: 1752

European-Non Finnish (NFE) AF: 0.0306 AC: 8247 AN: 269198

Other (OTH) AF: 0.0384 AC: 934 AN: 24344

GnomAD4 genome AF: 0.0358 AC: 5454 AN: 152300 Hom.: 218 Cov.: 32 AF XY: 0.0367 AC XY: 2733 AN XY: 74468

African (AFR) AF: 0.00791 AC: 329 AN: 41580

American (AMR) AF: 0.0646 AC: 989 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.193 AC: 998 AN: 5160

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4824

European-Finnish (FIN) AF: 0.00668 AC: 71 AN: 10624

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0362 AC: 2463 AN: 68012

Other (OTH) AF: 0.0529 AC: 112 AN: 2116

Alfa AF: 0.0415 Hom.: 577

Bravo AF: 0.0407

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs10817938; hg19: chr9-100462409;