rs1337038

chr13-74152427-A-G

Variant summary

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

The NM_001400153.1(KLF12):c.-32+153569T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,012 control chromosomes in the GnomAD database, including 13,147 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 0.37 (13147 hom., cov: 31)
• Consequence: KLF12 NM_001400153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910

Genes affected

KLF12 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF12	NM_001400153.1	c.-32+153569T>C		intron_variant
KLF12	NM_001400139.1	c.-32+153569T>C		intron_variant
KLF12	XM_011534909.3	c.-32+15722T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56060 AN: 151894 Hom.: 13142 Cov.: 31

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.369 AC: 56074 AN: 152012 Hom.: 13147 Cov.: 31 AF XY: 0.375 AC XY: 27839 AN XY: 74268

Gnomad4 AFR AF: 0.0877

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.369

Alfa AF: 0.423 Hom.: 2581

Bravo AF: 0.365

Asia WGS AF: 0.540 AC: 1879 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	7.7
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: rs1337038; hg19: chr13-74726564;