Variant 5-94417312-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001145678.3(KIAA0825):c.2551G>A(p.Ala851Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,549,286 control chromosomes in the GnomAD database, including 61,666 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4575 hom., cov: 33)

Exomes 𝑓: 0.28 ( 57091 hom. )

Consequence

KIAA0825
NM_001145678.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.169

Variant links:

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

KIAA0825 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024483502).

BP6

Variant 5-94417312-C-T is Benign according to our data. Variant chr5-94417312-C-T is described in ClinVar as [Benign]. Clinvar id is 1300066.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0825	NM_001145678.3 linkuse as main transcript	c.2551G>A	p.Ala851Thr	missense_variant	15/21	ENST00000682413.1	NP_001139150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0825	ENST00000682413.1 linkuse as main transcript	c.2551G>A	p.Ala851Thr	missense_variant	15/21		NM_001145678.3	ENSP00000506760	A1
KIAA0825	ENST00000504117.1 linkuse as main transcript	n.1413G>A		non_coding_transcript_exon_variant	9/9	1
KIAA0825	ENST00000703867.1 linkuse as main transcript	c.2566G>A	p.Ala856Thr	missense_variant	15/21			ENSP00000515512	P4
KIAA0825	ENST00000513200.7 linkuse as main transcript	c.2551G>A	p.Ala851Thr	missense_variant	14/20	5		ENSP00000424618	A1	Q8IV33-1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35373

AN:

151872

Hom.:

4580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.0734

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.231

GnomAD3 exomes

AF:

0.240

AC:

37493

AN:

155990

Hom.:

5152

AF XY:

0.246

AC XY:

20342

AN XY:

82670

show subpopulations

Gnomad AFR exome

AF:

0.155

Gnomad AMR exome

AF:

0.137

Gnomad ASJ exome

AF:

0.322

Gnomad EAS exome

AF:

0.0771

Gnomad SAS exome

AF:

0.248

Gnomad FIN exome

AF:

0.290

Gnomad NFE exome

AF:

0.294

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.280

AC:

390981

AN:

1397296

Hom.:

57091

Cov.:

AF XY:

0.280

AC XY:

192842

AN XY:

688992

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.321

Gnomad4 EAS exome

AF:

0.0682

Gnomad4 SAS exome

AF:

0.248

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.233

AC:

35374

AN:

151990

Hom.:

4575

Cov.:

AF XY:

0.229

AC XY:

17023

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.0724

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.282

Hom.:

15820

Bravo

AF:

0.219

TwinsUK

AF:

0.298

AC:

1105

ALSPAC

AF:

0.302

AC:

1165

ESP6500AA

AF:

0.148

AC:

205

ESP6500EA

AF:

0.295

AC:

940

ExAC

AF:

0.243

AC:

5858

Asia WGS

AF:

0.186

AC:

644

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Polydactyly, postaxial, type a10

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

KIAA0825-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 04, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.0055

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.25

FATHMM_MKL

Benign

0.60

LIST_S2

Benign

0.61

MetaRNN

Benign

0.0024

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

MutationTaster

Benign

0.80

P;P;P

PrimateAI

Benign

0.34

PROVEAN

Benign

0.090

REVEL

Benign

0.057

Sift

Benign

0.30

Sift4G

Benign

0.46

Polyphen

0.26

Vest4

0.029

ClinPred

0.020

GERP RS

3.6

Varity_R

0.039

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over