11-65726789-G-T

Variant names:

• chr11-65726789-G-T
• rs478304
• ENST00000534154.1:n.-150G>T

Variant summary

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

The ENST00000534154.1(KRT8P26):​n.-150G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 165,696 control chromosomes in the GnomAD database, including 23,896 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 0.54 (22301 hom., cov: 32)
  • Exomes 𝑓: 0.46 (1595 hom.)
• Consequence: KRT8P26 ENST00000534154.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

KRT8P26 (HGNC:33378): (keratin 8 pseudogene 26)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT8P26	ENST00000534154.1	n.-150G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81453 AN: 151954 Hom.: 22274 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.542

GnomAD4 exome AF: 0.456 AC: 6211 AN: 13624 Hom.: 1595 AF XY: 0.431 AC XY: 2962 AN XY: 6872

Gnomad4 AFR exome AF: 0.557

Gnomad4 AMR exome AF: 0.651

Gnomad4 ASJ exome AF: 0.370

Gnomad4 EAS exome AF: 0.453

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.450

Gnomad4 NFE exome AF: 0.477

Gnomad4 OTH exome AF: 0.481

GnomAD4 genome AF: 0.536 AC: 81525 AN: 152072 Hom.: 22301 Cov.: 32 AF XY: 0.527 AC XY: 39133 AN XY: 74322

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.539

Alfa AF: 0.518 Hom.: 2541

Bravo AF: 0.562

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs478304; hg19: chr11-65494260;