Variant 5-94464955-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_001145678.3(KIAA0825):c.1977A>G(p.Leu659=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0169 in 1,551,666 control chromosomes in the GnomAD database, including 242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.014 ( 18 hom., cov: 32)

Exomes 𝑓: 0.017 ( 224 hom. )

Consequence

KIAA0825
NM_001145678.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.592

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 (BayesDel_noAF=-0.78).

BP6

Variant 5-94464955-T-C is Benign according to our data. Variant chr5-94464955-T-C is described in ClinVar as [Benign]. Clinvar id is 3037527.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.592 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0135 (2062/152282) while in subpopulation NFE AF= 0.0211 (1432/68020). AF 95% confidence interval is 0.0201. There are 18 homozygotes in gnomad4. There are 994 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0825	NM_001145678.3 linkuse as main transcript	c.1977A>G	p.Leu659=	synonymous_variant	11/21	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.1977A>G	p.Leu659=	synonymous_variant	11/21		NM_001145678.3	ENSP00000506760	A1
KIAA0825	ENST00000504117.1 linkuse as main transcript	n.824A>G		non_coding_transcript_exon_variant	5/9	1
KIAA0825	ENST00000703867.1 linkuse as main transcript	c.1977A>G	p.Leu659=	synonymous_variant	11/21			ENSP00000515512	P4
KIAA0825	ENST00000513200.7 linkuse as main transcript	c.1977A>G	p.Leu659=	synonymous_variant	10/20	5		ENSP00000424618	A1	Q8IV33-1

Frequencies

GnomAD3 genomes

AF:

0.0136

AC:

2063

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00343

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0158

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.00867

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0210

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0136

AC:

2131

AN:

156732

Hom.:

AF XY:

0.0141

AC XY:

1168

AN XY:

83058

show subpopulations

Gnomad AFR exome

AF:

0.00315

Gnomad AMR exome

AF:

0.00940

Gnomad ASJ exome

AF:

0.0106

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0159

Gnomad FIN exome

AF:

0.00909

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0164

GnomAD4 exome

AF:

0.0173

AC:

24189

AN:

1399384

Hom.:

224

Cov.:

AF XY:

0.0174

AC XY:

12015

AN XY:

690204

show subpopulations

Gnomad4 AFR exome

AF:

0.00237

Gnomad4 AMR exome

AF:

0.00972

Gnomad4 ASJ exome

AF:

0.00858

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0161

Gnomad4 FIN exome

AF:

0.00881

Gnomad4 NFE exome

AF:

0.0192

Gnomad4 OTH exome

AF:

0.0169

GnomAD4 genome

AF:

0.0135

AC:

2062

AN:

152282

Hom.:

Cov.:

AF XY:

0.0133

AC XY:

994

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00342

Gnomad4 AMR

AF:

0.0158

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0145

Gnomad4 FIN

AF:

0.00867

Gnomad4 NFE

AF:

0.0211

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.0162

Hom.:

Bravo

AF:

0.0131

Asia WGS

AF:

0.00808

AC:

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 06, 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

-0.78

CADD

Benign

3.2

DANN

Benign

0.63

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