rs9838915

Variant summary

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

The NM_014079.4(KLF15):​c.1083-3482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,120 control chromosomes in the GnomAD database, including 3,058 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 0.19 ( 3058 hom., cov: 32)

Consequence

KLF15
NM_014079.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242
Variant links:
Genes affected
KLF15 (HGNC:14536): (KLF transcription factor 15) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of peptidyl-lysine acetylation and positive regulation of transcription by RNA polymerase II. Located in nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KLF15NM_014079.4 linkuse as main transcriptc.1083-3482C>T intron_variant ENST00000296233.4 NP_054798.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KLF15ENST00000296233.4 linkuse as main transcriptc.1083-3482C>T intron_variant 1 NM_014079.4 ENSP00000296233 P1

Frequencies

GnomAD3 genomes
AF:
0.191
AC:
29098
AN:
152002
Hom.:
3049
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.170
Gnomad AMI
AF:
0.197
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.162
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.307
Gnomad FIN
AF:
0.141
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.174
Gnomad OTH
AF:
0.201
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.192
AC:
29134
AN:
152120
Hom.:
3058
Cov.:
32
AF XY:
0.199
AC XY:
14768
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.170
Gnomad4 AMR
AF:
0.306
Gnomad4 ASJ
AF:
0.162
Gnomad4 EAS
AF:
0.269
Gnomad4 SAS
AF:
0.306
Gnomad4 FIN
AF:
0.141
Gnomad4 NFE
AF:
0.174
Gnomad4 OTH
AF:
0.203
Alfa
AF:
0.183
Hom.:
3621
Bravo
AF:
0.198
Asia WGS
AF:
0.253
AC:
880
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.5
DANN
Benign
0.50

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: rs9838915; hg19: chr3-126066220; COSMIC: COSV56179692; API