rs9838915

chr3-126347377-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

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]

ACMG classification

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	UniProt
KLF15	NM_014079.4	c.1083-3482C>T		intron_variant		ENST00000296233.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF15	ENST00000296233.4	c.1083-3482C>T		intron_variant		1	NM_014079.4	P1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29098 AN: 152002 Hom.: 3049 Cov.: 32

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

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

Other links and lift over

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