Genetic Variant KRI1:p.Ala572Ala (chr19-10555152-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_023008.5(KRI1):c.1716G>A(p.Ala572Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 1,612,708 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 1 hom., cov: 34)

Exomes 𝑓: 0.0034 ( 13 hom. )

Consequence

KRI1
NM_023008.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.74

Publications

2 publications found

Variant links:

Genes affected

KRI1 (HGNC:25769): (KRI1 homolog) This gene overlaps with the gene for cysteine endopeptidase AUT-like 4 in a head-to-tail orientation. [provided by RefSeq, Jul 2008]

KRI1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 19-10555152-C-T is Benign according to our data. Variant chr19-10555152-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2649297.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.74 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 13 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_023008.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRI1	NM_023008.5	MANE Select	c.1716G>A	p.Ala572Ala	synonymous	Exon 18 of 19	NP_075384.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KRI1	ENST00000312962.12	TSL:1 MANE Select	c.1716G>A	p.Ala572Ala	synonymous	Exon 18 of 19	ENSP00000320917.9	Q8N9T8
KRI1	ENST00000906782.1		c.1758G>A	p.Ala586Ala	synonymous	Exon 18 of 19	ENSP00000576841.1
KRI1	ENST00000958127.1		c.1740G>A	p.Ala580Ala	synonymous	Exon 18 of 19	ENSP00000628186.1

Frequencies

GnomAD3 genomes

AF:

0.00317

AC:

478

AN:

150812

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000900

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00517

Gnomad ASJ

AF:

0.00694

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00275

Gnomad FIN

AF:

0.00526

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00385

Gnomad OTH

AF:

0.00484

GnomAD2 exomes

AF:

0.00314

AC:

790

AN:

251246

AF XY:

0.00325

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00266

Gnomad ASJ exome

AF:

0.00665

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.00351

Gnomad NFE exome

AF:

0.00354

Gnomad OTH exome

AF:

0.00571

GnomAD4 exome

AF:

0.00344

AC:

5022

AN:

1461780

Hom.:

Cov.:

AF XY:

0.00342

AC XY:

2484

AN XY:

727210

show subpopulations

African (AFR)

AF:

0.000657

AC:

AN:

33480

American (AMR)

AF:

0.00295

AC:

132

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.00704

AC:

184

AN:

26132

East Asian (EAS)

AF:

0.00

AC:

AN:

39696

South Asian (SAS)

AF:

0.00370

AC:

319

AN:

86256

European-Finnish (FIN)

AF:

0.00277

AC:

148

AN:

53366

Middle Eastern (MID)

AF:

0.00330

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00360

AC:

4008

AN:

1111976

Other (OTH)

AF:

0.00315

AC:

190

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

267

534

802

1069

1336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00317

AC:

478

AN:

150928

Hom.:

Cov.:

AF XY:

0.00323

AC XY:

238

AN XY:

73684

show subpopulations

African (AFR)

AF:

0.000897

AC:

AN:

41250

American (AMR)

AF:

0.00517

AC:

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.00694

AC:

AN:

3458

East Asian (EAS)

AF:

0.00

AC:

AN:

5062

South Asian (SAS)

AF:

0.00275

AC:

AN:

4726

European-Finnish (FIN)

AF:

0.00526

AC:

AN:

10462

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00385

AC:

260

AN:

67584

Other (OTH)

AF:

0.00479

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

101

126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00319

Hom.:

Bravo

AF:

0.00292

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00433

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.078

(source)

DANN

Benign

0.87

PhyloP100

-4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over