Variant 19-10555152-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000312962.12(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
ENST00000312962.12 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.74

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:

KRI1 (HGNC:):

KRI1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRI1	NM_023008.5 linkuse as main transcript	c.1716G>A	p.Ala572Ala	synonymous_variant	18/19	ENST00000312962.12	NP_075384.4	Q8N9T8A0A494C108
KRI1	XM_047439232.1 linkuse as main transcript	c.1722G>A	p.Ala574Ala	synonymous_variant	17/18		XP_047295188.1
KRI1	XM_011528190.3 linkuse as main transcript	c.1380G>A	p.Ala460Ala	synonymous_variant	17/18		XP_011526492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRI1	ENST00000312962.12 linkuse as main transcript	c.1716G>A	p.Ala572Ala	synonymous_variant	18/19	1	NM_023008.5	ENSP00000320917.9		Q8N9T8

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

GnomAD3 exomes

AF:

0.00314

AC:

790

AN:

251246

Hom.:

AF XY:

0.00325

AC XY:

442

AN XY:

135808

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 SAS exome

AF:

0.00350

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

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.00295

Gnomad4 ASJ exome

AF:

0.00704

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00370

Gnomad4 FIN exome

AF:

0.00277

Gnomad4 NFE exome

AF:

0.00360

Gnomad4 OTH exome

AF:

0.00315

GnomAD4 genome

AF:

0.00317

AC:

478

AN:

150928

Hom.:

Cov.:

AF XY:

0.00323

AC XY:

238

AN XY:

73684

show subpopulations

Gnomad4 AFR

AF:

0.000897

Gnomad4 AMR

AF:

0.00517

Gnomad4 ASJ

AF:

0.00694

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00275

Gnomad4 FIN

AF:

0.00526

Gnomad4 NFE

AF:

0.00385

Gnomad4 OTH

AF:

0.00479

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

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

KRI1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.078

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over