Variant rs2070875 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000224.3(KRT18):c.500+124G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 839,932 control chromosomes in the GnomAD database, including 12,826 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 0.085 ( 1658 hom., cov: 32)

Exomes 𝑓: 0.092 ( 11168 hom. )

Consequence

KRT18
NM_000224.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.894

Variant links:

Genes affected

KRT18 (HGNC:6430): (keratin 18) KRT18 encodes the type I intermediate filament chain keratin 18. Keratin 18, together with its filament partner keratin 8, are perhaps the most commonly found members of the intermediate filament gene family. They are expressed in single layer epithelial tissues of the body. Mutations in this gene have been linked to cryptogenic cirrhosis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

KRT18 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRT18	NM_000224.3 linkuse as main transcript	c.500+124G>T		intron_variant		ENST00000388835.4
KRT18	NM_199187.2 linkuse as main transcript	c.500+124G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT18	ENST00000388835.4 linkuse as main transcript	c.500+124G>T		intron_variant		1	NM_000224.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0849

AC:

12911

AN:

151998

Hom.:

1648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0941

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.0353

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0129

Gnomad OTH

AF:

0.0900

GnomAD4 exome

AF:

0.0925

AC:

63590

AN:

687816

Hom.:

11168

Cov.:

AF XY:

0.0927

AC XY:

34217

AN XY:

369252

show subpopulations

Gnomad4 AFR exome

AF:

0.0972

Gnomad4 AMR exome

AF:

0.392

Gnomad4 ASJ exome

AF:

0.0297

Gnomad4 EAS exome

AF:

0.538

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.0336

Gnomad4 NFE exome

AF:

0.0138

Gnomad4 OTH exome

AF:

0.0795

GnomAD4 genome

AF:

0.0850

AC:

12937

AN:

152116

Hom.:

1658

Cov.:

AF XY:

0.0938

AC XY:

6975

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0940

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.0323

Gnomad4 EAS

AF:

0.550

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.0353

Gnomad4 NFE

AF:

0.0129

Gnomad4 OTH

AF:

0.0975

Alfa

AF:

0.0461

Hom.:

Bravo

AF:

0.104

Asia WGS

AF:

0.341

AC:

1185

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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