rs9838915

Variant names:

• chr3-126347377-G-A
• rs9838915
• NM_014079.4:c.1083-3482C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014079.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF15	NM_014079.4	MANE Select	c.1083-3482C>T		intron	N/A	NP_054798.1	Q9UIH9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF15	ENST00000296233.4	TSL:1 MANE Select	c.1083-3482C>T		intron	N/A	ENSP00000296233.3	Q9UIH9
	KLF15	ENST00000892073.1		c.1083-3482C>T		intron	N/A	ENSP00000562132.1
	KLF15	ENST00000892074.1		c.1083-3482C>T		intron	N/A	ENSP00000562133.1

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

African (AFR) AF: 0.170 AC: 7076 AN: 41504

American (AMR) AF: 0.306 AC: 4675 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1390 AN: 5158

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4816

European-Finnish (FIN) AF: 0.141 AC: 1499 AN: 10596

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11798 AN: 67984

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.182 Hom.: 8056

Bravo AF: 0.198

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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