rs12552044

chr9-70452722-T-C

Variant summary

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

The XR_001746707.3(KLF9-DT):n.222-9427T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,114 control chromosomes in the GnomAD database, including 37,333 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 0.69 (37333 hom., cov: 33)
• Consequence: KLF9-DT XR_001746707.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

KLF9-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF9-DT	XR_001746707.3	n.222-9427T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105576 AN: 151996 Hom.: 37304 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.695 AC: 105648 AN: 152114 Hom.: 37333 Cov.: 33 AF XY: 0.696 AC XY: 51783 AN XY: 74360

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.694

Alfa AF: 0.722 Hom.: 8105

Bravo AF: 0.685

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12552044; hg19: chr9-73067638;