rs11884397

Variant summary

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

The NM_052920.2(KLHL29):​c.940+19668G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,178 control chromosomes in the GnomAD database, including 924 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 0.10 ( 924 hom., cov: 33)

Consequence

KLHL29
NM_052920.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88
Variant links:
Genes affected
KLHL29 (HGNC:29404): (kelch like family member 29)

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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KLHL29NM_052920.2 linkuse as main transcriptc.940+19668G>A intron_variant ENST00000486442.6
KLHL29XM_006711929.4 linkuse as main transcriptc.940+19668G>A intron_variant
KLHL29XM_011532501.3 linkuse as main transcriptc.22+17414G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KLHL29ENST00000486442.6 linkuse as main transcriptc.940+19668G>A intron_variant 5 NM_052920.2 P1Q96CT2-1
KLHL29ENST00000288548.5 linkuse as main transcriptc.459+19668G>A intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15543
AN:
152060
Hom.:
922
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.128
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.0608
Gnomad ASJ
AF:
0.0764
Gnomad EAS
AF:
0.162
Gnomad SAS
AF:
0.138
Gnomad FIN
AF:
0.160
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0824
Gnomad OTH
AF:
0.0851
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15552
AN:
152178
Hom.:
924
Cov.:
33
AF XY:
0.105
AC XY:
7826
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.0606
Gnomad4 ASJ
AF:
0.0764
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.138
Gnomad4 FIN
AF:
0.160
Gnomad4 NFE
AF:
0.0823
Gnomad4 OTH
AF:
0.0847
Alfa
AF:
0.0887
Hom.:
323
Bravo
AF:
0.0954
Asia WGS
AF:
0.152
AC:
530
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.29
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs11884397; hg19: chr2-23885388; API