rs12429889

chr13-74168185-T-C

Variant summary

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

The NM_001400153.1(KLF12):c.-32+137811A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,198 control chromosomes in the GnomAD database, including 9,523 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 0.28 (9523 hom., cov: 32)
• Consequence: KLF12 NM_001400153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

Genes affected

KLF12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF12	NM_001400153.1	c.-32+137811A>G		intron_variant
KLF12	XM_011534909.3	c.-68A>G		5_prime_UTR_variant	1/8
KLF12	NM_001400139.1	c.-32+137811A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42595 AN: 152080 Hom.: 9495 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42673 AN: 152198 Hom.: 9523 Cov.: 32 AF XY: 0.275 AC XY: 20475 AN XY: 74422

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0749

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.271

Alfa AF: 0.164 Hom.: 2106

Bravo AF: 0.300

Asia WGS AF: 0.243 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.5
Dann	Benign	0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12429889; hg19: chr13-74742322;