Variant 5-94386345-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001145678.3(KIAA0825):c.3516C>A(p.Ile1172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,550,736 control chromosomes in the GnomAD database, including 17,418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1472 hom., cov: 32)

Exomes 𝑓: 0.15 ( 15946 hom. )

Consequence

KIAA0825
NM_001145678.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.526

Variant links:

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

KIAA0825 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 5-94386345-G-T is Benign according to our data. Variant chr5-94386345-G-T is described in ClinVar as [Benign]. Clinvar id is 3057167.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.526 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 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.3516C>A	p.Ile1172=	synonymous_variant	19/21	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.3516C>A	p.Ile1172=	synonymous_variant	19/21		NM_001145678.3	ENSP00000506760	A1
KIAA0825	ENST00000703867.1 linkuse as main transcript	c.3531C>A	p.Ile1177=	synonymous_variant	19/21			ENSP00000515512	P4
KIAA0825	ENST00000513200.7 linkuse as main transcript	c.3516C>A	p.Ile1172=	synonymous_variant	18/20	5		ENSP00000424618	A1	Q8IV33-1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20392

AN:

152032

Hom.:

1472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.0987

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.130

AC:

20521

AN:

157864

Hom.:

1551

AF XY:

0.136

AC XY:

11333

AN XY:

83314

show subpopulations

Gnomad AFR exome

AF:

0.130

Gnomad AMR exome

AF:

0.0753

Gnomad ASJ exome

AF:

0.176

Gnomad EAS exome

AF:

0.000367

Gnomad SAS exome

AF:

0.182

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.146

AC:

204286

AN:

1398586

Hom.:

15946

Cov.:

AF XY:

0.148

AC XY:

101825

AN XY:

689786

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.0794

Gnomad4 ASJ exome

AF:

0.171

Gnomad4 EAS exome

AF:

0.000588

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.134

AC:

20410

AN:

152150

Hom.:

1472

Cov.:

AF XY:

0.131

AC XY:

9731

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.0985

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.00328

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.112

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.147

Hom.:

4118

Bravo

AF:

0.130

Asia WGS

AF:

0.0830

AC:

288

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KIAA0825-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 19, 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

BayesDel_noAF

Benign

-0.67

CADD

Benign

2.2

DANN

Benign

0.66

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