rs10817938

chr9-97700127-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCSC2	NR_147055.1	n.1501-56A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT18P13	ENST00000400056.3	n.683T>C		non_coding_transcript_exon_variant	2/2
PTCSC2	ENST00000649461.1	n.1501-56A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.00797

Gnomad4 AMR exome AF: 0.0718

Gnomad4 ASJ exome AF: 0.0310

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.0515

Gnomad4 FIN exome AF: 0.00480

Gnomad4 NFE exome AF: 0.0306

Gnomad4 OTH exome AF: 0.0384

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

Gnomad4 AFR AF: 0.00791

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.00668

Gnomad4 NFE AF: 0.0362

Gnomad4 OTH AF: 0.0529

Alfa AF: 0.0405 Hom.: 164

Bravo AF: 0.0407

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	1.3
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817938; hg19: chr9-100462409;