rs963265

chr9-70479619-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.390-15015T>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 0.362 in 150,782 control chromosomes in the GnomAD database, including 10,419 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 0.36 (10419 hom., cov: 32)
• Consequence: KLF9-DT XR_001746707.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

KLF9-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF9-DT	XR_001746707.3	n.390-15015T>C		intron_variant, non_coding_transcript_variant
KLF9-DT	XR_001746708.3	n.390-15015T>C		intron_variant, non_coding_transcript_variant
KLF9-DT	XR_001746709.3	n.389+16764T>C		intron_variant, non_coding_transcript_variant
KLF9-DT	XR_001746710.3	n.389+16764T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54549 AN: 150674 Hom.: 10413 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.362 AC: 54578 AN: 150782 Hom.: 10419 Cov.: 32 AF XY: 0.357 AC XY: 26324 AN XY: 73722

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.360

Alfa AF: 0.401 Hom.: 2999

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.0
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963265; hg19: chr9-73094535;