Variant rs11540407 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007043.7(KRR1):c.401G>A(p.Arg134Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,477,928 control chromosomes in the GnomAD database, including 46,544 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.24 ( 3814 hom., cov: 25)

Exomes 𝑓: 0.23 ( 42730 hom. )

Consequence

KRR1
NM_007043.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.30

Variant links:

Genes affected

KRR1 (HGNC:5176): (KRR1 small subunit processome component homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in chromosome; intercellular bridge; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

KRR1 links:

KRR1 (HGNC:):

KRR1 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 (MetaRNN=0.0018532872).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRR1	NM_007043.7 linkuse as main transcript	c.401G>A	p.Arg134Gln	missense_variant	4/10	ENST00000229214.9	NP_008974.5	Q13601-1
KRR1	XM_047428133.1 linkuse as main transcript	c.107G>A	p.Arg36Gln	missense_variant	4/10		XP_047284089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KRR1	ENST00000229214.9 linkuse as main transcript	c.401G>A	p.Arg134Gln	missense_variant	4/10	1	NM_007043.7	ENSP00000229214.4	Q13601-1
KRR1	ENST00000438169.6 linkuse as main transcript	c.401G>A	p.Arg134Gln	missense_variant	4/9	1		ENSP00000411740.2	Q13601-2
KRR1	ENST00000550023.5 linkuse as main transcript	n.417G>A		non_coding_transcript_exon_variant	4/4	2
KRR1	ENST00000550898.1 linkuse as main transcript	n.612G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

31765

AN:

133132

Hom.:

3810

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.308

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.246

AC:

49408

AN:

201184

Hom.:

6476

AF XY:

0.248

AC XY:

27343

AN XY:

110342

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.109

Gnomad SAS exome

AF:

0.323

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.234

AC:

314607

AN:

1344758

Hom.:

42730

Cov.:

AF XY:

0.237

AC XY:

158788

AN XY:

669106

show subpopulations

Gnomad4 AFR exome

AF:

0.193

Gnomad4 AMR exome

AF:

0.324

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.312

Gnomad4 FIN exome

AF:

0.198

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.237

GnomAD4 genome

AF:

0.239

AC:

31776

AN:

133170

Hom.:

3814

Cov.:

AF XY:

0.238

AC XY:

15174

AN XY:

63716

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.120

Gnomad4 SAS

AF:

0.342

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.250

Hom.:

9853

Bravo

AF:

0.238

TwinsUK

AF:

0.231

AC:

856

ALSPAC

AF:

0.236

AC:

910

ESP6500AA

AF:

0.203

AC:

895

ESP6500EA

AF:

0.248

AC:

2131

ExAC

AF:

0.254

AC:

30833

Asia WGS

AF:

0.218

AC:

752

AN:

3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.30

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.25

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.61

D;.

Eigen

Pathogenic

0.79

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.88

D;D

MetaRNN

Benign

0.0019

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

2.9

M;M

PrimateAI

Uncertain

0.69

PROVEAN

Uncertain

-2.8

D;D

REVEL

Uncertain

0.30

Sift

Uncertain

0.015

D;D

Sift4G

Uncertain

0.0090

D;D

Polyphen

1.0

D;.

Vest4

0.50

MPC

0.35

ClinPred

0.023

GERP RS

4.6

Varity_R

0.57

gMVP

0.83

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