rs4747796

Positions:

• chr10-8514192-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451609.1(KRT8P37):​n.915C>T 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 0.45 in 747,432 control chromosomes in the GnomAD database, including 77,504 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 0.44 (14776 hom., cov: 32)
  • Exomes 𝑓: 0.45 (62728 hom.)
• Consequence: KRT8P37 ENST00000451609.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

KRT8P37 (HGNC:39871): (keratin 8 pseudogene 37)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRT8P37	ENST00000451609.1	n.915C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66166 AN: 151998 Hom.: 14773 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.454 AC: 270262 AN: 595314 Hom.: 62728 Cov.: 5 AF XY: 0.453 AC XY: 146247 AN XY: 322916

Gnomad4 AFR exome AF: 0.334

Gnomad4 AMR exome AF: 0.465

Gnomad4 ASJ exome AF: 0.454

Gnomad4 EAS exome AF: 0.294

Gnomad4 SAS exome AF: 0.398

Gnomad4 FIN exome AF: 0.479

Gnomad4 NFE exome AF: 0.482

Gnomad4 OTH exome AF: 0.452

GnomAD4 genome AF: 0.435 AC: 66174 AN: 152118 Hom.: 14776 Cov.: 32 AF XY: 0.434 AC XY: 32285 AN XY: 74354

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.437

Alfa AF: 0.458 Hom.: 2015

Bravo AF: 0.434

Asia WGS AF: 0.378 AC: 1316 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	1.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4747796; hg19: chr10-8556155;