Genetic Variant KIAA0825:p.Ser1039Ser (chr5-94396280-A-G) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001145678.3(KIAA0825):c.3117T>C(p.Ser1039Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 1,551,326 control chromosomes in the GnomAD database, including 670,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.94 ( 67688 hom., cov: 32)

Exomes 𝑓: 0.93 ( 602620 hom. )

Consequence

KIAA0825
NM_001145678.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.350

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 5-94396280-A-G is Benign according to our data. Variant chr5-94396280-A-G is described in ClinVar as [Benign]. Clinvar id is 1300065.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0825	NM_001145678.3 link	c.3117T>C	p.Ser1039Ser	synonymous_variant	Exon 17 of 21	ENST00000682413.1	NP_001139150.1	A0A804HHT9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIAA0825	ENST00000682413.1 link	c.3117T>C	p.Ser1039Ser	synonymous_variant	Exon 17 of 21		NM_001145678.3	ENSP00000506760.1	A0A804HHT9
KIAA0825	ENST00000703867.1 link	c.3132T>C	p.Ser1044Ser	synonymous_variant	Exon 17 of 21			ENSP00000515512.1	A0A994J718
KIAA0825	ENST00000513200.7 link	c.3117T>C	p.Ser1039Ser	synonymous_variant	Exon 16 of 20	5		ENSP00000424618.2	Q8IV33-1

Frequencies

GnomAD3 genomes

AF:

0.942

AC:

143370

AN:

152152

Hom.:

67623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.984

Gnomad AMI

AF:

0.864

Gnomad AMR

AF:

0.947

Gnomad ASJ

AF:

0.889

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.953

Gnomad FIN

AF:

0.896

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.922

Gnomad OTH

AF:

0.944

GnomAD3 exomes

AF:

0.937

AC:

146736

AN:

156588

Hom.:

68826

AF XY:

0.936

AC XY:

77458

AN XY:

82790

show subpopulations

Gnomad AFR exome

AF:

0.985

Gnomad AMR exome

AF:

0.961

Gnomad ASJ exome

AF:

0.889

Gnomad EAS exome

AF:

0.999

Gnomad SAS exome

AF:

0.951

Gnomad FIN exome

AF:

0.894

Gnomad NFE exome

AF:

0.924

Gnomad OTH exome

AF:

0.929

GnomAD4 exome

AF:

0.928

AC:

1298217

AN:

1399056

Hom.:

602620

Cov.:

AF XY:

0.928

AC XY:

640347

AN XY:

689986

show subpopulations

Gnomad4 AFR exome

AF:

0.985

Gnomad4 AMR exome

AF:

0.959

Gnomad4 ASJ exome

AF:

0.889

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.950

Gnomad4 FIN exome

AF:

0.894

Gnomad4 NFE exome

AF:

0.923

Gnomad4 OTH exome

AF:

0.934

GnomAD4 genome

AF:

0.942

AC:

143495

AN:

152270

Hom.:

67688

Cov.:

AF XY:

0.943

AC XY:

70169

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.984

Gnomad4 AMR

AF:

0.947

Gnomad4 ASJ

AF:

0.889

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.954

Gnomad4 FIN

AF:

0.896

Gnomad4 NFE

AF:

0.922

Gnomad4 OTH

AF:

0.945

Alfa

AF:

0.925

Hom.:

99601

Bravo

AF:

0.949

Asia WGS

AF:

0.978

AC:

3403

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Polydactyly, postaxial, type a10

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

KIAA0825-related disorder

Benign:1

Oct 29, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.62

CADD

Benign

DANN

Benign

0.70

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