rs6067284

chr20-49957917-G-Achr20-49957917-G-T

Variant summary

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

The ENST00000422599.1(KRT18P4):n.1173G>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 0.413 in 752,374 control chromosomes in the GnomAD database, including 68,862 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 0.35 (11035 hom., cov: 30)
  • Exomes 𝑓: 0.43 (57827 hom.)
• Consequence: KRT18P4 ENST00000422599.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

KRT18P4 (HGNC:16604): (keratin 18 pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT18P4	ENST00000422599.1	n.1173G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53097 AN: 151680 Hom.: 11019 Cov.: 30

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.429 AC: 257729 AN: 600576 Hom.: 57827 Cov.: 5 AF XY: 0.437 AC XY: 142718 AN XY: 326852

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.490

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.340

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.558

Gnomad4 NFE exome AF: 0.418

Gnomad4 OTH exome AF: 0.398

GnomAD4 genome AF: 0.350 AC: 53147 AN: 151798 Hom.: 11035 Cov.: 30 AF XY: 0.364 AC XY: 26977 AN XY: 74134

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.359

Alfa AF: 0.270 Hom.: 802

Bravo AF: 0.324

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	7.2
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6067284; hg19: chr20-48574454; COSMIC: COSV54869430;