Variant rs6067284 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

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

KRT18P4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53097

AN:

151680

Hom.:

11019

Cov.:

show subpopulations

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.:

AF XY:

0.437

AC XY:

142718

AN XY:

326852

show subpopulations

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.:

AF XY:

0.364

AC XY:

26977

AN XY:

74134

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over