Variant 5-94417355-G-A 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.2508C>T(p.Ser836=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,541,882 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0034 ( 26 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 79 hom. )

Consequence

KIAA0825
NM_001145678.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.664

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=-0.78).

BP6

Variant 5-94417355-G-A is Benign according to our data. Variant chr5-94417355-G-A is described in ClinVar as [Benign]. Clinvar id is 3038502.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.664 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0641 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.2508C>T	p.Ser836=	synonymous_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.2508C>T	p.Ser836=	synonymous_variant	15/21		NM_001145678.3	ENSP00000506760	A1
KIAA0825	ENST00000504117.1 linkuse as main transcript	n.1370C>T		non_coding_transcript_exon_variant	9/9	1
KIAA0825	ENST00000703867.1 linkuse as main transcript	c.2523C>T	p.Ser841=	synonymous_variant	15/21			ENSP00000515512	P4
KIAA0825	ENST00000513200.7 linkuse as main transcript	c.2508C>T	p.Ser836=	synonymous_variant	14/20	5		ENSP00000424618	A1	Q8IV33-1

Frequencies

GnomAD3 genomes

AF:

0.00343

AC:

521

AN:

152020

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0702

Gnomad SAS

AF:

0.00685

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00506

AC:

785

AN:

155088

Hom.:

AF XY:

0.00493

AC XY:

405

AN XY:

82212

show subpopulations

Gnomad AFR exome

AF:

0.000759

Gnomad AMR exome

AF:

0.000123

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0657

Gnomad SAS exome

AF:

0.00150

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000151

Gnomad OTH exome

AF:

0.00438

GnomAD4 exome

AF:

0.00184

AC:

2563

AN:

1389744

Hom.:

Cov.:

AF XY:

0.00186

AC XY:

1271

AN XY:

683656

show subpopulations

Gnomad4 AFR exome

AF:

0.000446

Gnomad4 AMR exome

AF:

0.000169

Gnomad4 ASJ exome

AF:

0.0000799

Gnomad4 EAS exome

AF:

0.0534

Gnomad4 SAS exome

AF:

0.00242

Gnomad4 FIN exome

AF:

0.000163

Gnomad4 NFE exome

AF:

0.0000999

Gnomad4 OTH exome

AF:

0.00576

GnomAD4 genome

AF:

0.00342

AC:

520

AN:

152138

Hom.:

Cov.:

AF XY:

0.00355

AC XY:

264

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.00205

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0700

Gnomad4 SAS

AF:

0.00707

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000162

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.000665

Hom.:

Bravo

AF:

0.00301

Asia WGS

AF:

0.0410

AC:

142

AN:

3476

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

Jul 10, 2024

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

9.2

DANN

Benign

0.49

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