rs13163610

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001145678.3(KIAA0825):​c.3711-59048T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,558 control chromosomes in the GnomAD database, including 954 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 954 hom., cov: 32)

Consequence

KIAA0825
NM_001145678.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.135
Variant links:
Genes affected
KIAA0825 (HGNC:28532): (KIAA0825)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIAA0825NM_001145678.3 linkuse as main transcriptc.3711-59048T>G intron_variant ENST00000682413.1 NP_001139150.1
LOC105379087XR_001742443.2 linkuse as main transcriptn.315-4213A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIAA0825ENST00000682413.1 linkuse as main transcriptc.3711-59048T>G intron_variant NM_001145678.3 ENSP00000506760 A1
KIAA0825ENST00000513200.7 linkuse as main transcriptc.3711-59048T>G intron_variant 5 ENSP00000424618 A1Q8IV33-1
KIAA0825ENST00000703867.1 linkuse as main transcriptc.3726-59048T>G intron_variant ENSP00000515512 P4

Frequencies

GnomAD3 genomes
AF:
0.105
AC:
15958
AN:
151440
Hom.:
950
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.107
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.0861
Gnomad ASJ
AF:
0.192
Gnomad EAS
AF:
0.0454
Gnomad SAS
AF:
0.0709
Gnomad FIN
AF:
0.0290
Gnomad MID
AF:
0.150
Gnomad NFE
AF:
0.123
Gnomad OTH
AF:
0.119
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.105
AC:
15985
AN:
151558
Hom.:
954
Cov.:
32
AF XY:
0.101
AC XY:
7448
AN XY:
74058
show subpopulations
Gnomad4 AFR
AF:
0.107
Gnomad4 AMR
AF:
0.0860
Gnomad4 ASJ
AF:
0.192
Gnomad4 EAS
AF:
0.0453
Gnomad4 SAS
AF:
0.0711
Gnomad4 FIN
AF:
0.0290
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.119
Alfa
AF:
0.116
Hom.:
1459
Bravo
AF:
0.110
Asia WGS
AF:
0.0760
AC:
266
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
6.2
DANN
Benign
0.31

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.

Other links and lift over

dbSNP: rs13163610; hg19: chr5-93548877; COSMIC: COSV70247292; API