rs8000245

chr13-74156255-C-T

Variant summary

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

The NM_001400153.1(KLF12):c.-32+149741G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,120 control chromosomes in the GnomAD database, including 2,917 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 0.18 (2917 hom., cov: 32)
• Consequence: KLF12 NM_001400153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

KLF12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF12	NM_001400153.1	c.-32+149741G>A		intron_variant
KLF12	NM_001400139.1	c.-32+149741G>A		intron_variant
KLF12	XM_011534909.3	c.-32+11894G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27373 AN: 152002 Hom.: 2909 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.180 AC: 27409 AN: 152120 Hom.: 2917 Cov.: 32 AF XY: 0.181 AC XY: 13429 AN XY: 74388

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0955

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.176

Alfa AF: 0.139 Hom.: 2412

Bravo AF: 0.180

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.3
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8000245; hg19: chr13-74730392;