chr9-70450096-T-A

Variant names:

• chr9-70450096-T-A
• rs878724
• ENST00000833041.1:n.353-12053T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000833041.1(ENSG00000308298):​n.353-12053T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,028 control chromosomes in the GnomAD database, including 38,591 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 0.71 (38591 hom., cov: 31)
• Consequence: ENSG00000308298 ENST00000833041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 0 publications found

Genes affected

ENSG00000308298 (HGNC:):

KLF9-DT (HGNC:54815): (KLF9 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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 rank	MANE	Protein	UniProt
KLF9-DT	XR_001746707.3	n.222-12053T>A		intron_variant	Intron 1 of 4
KLF9-DT	XR_001746708.3	n.222-12053T>A		intron_variant	Intron 1 of 4
KLF9-DT	XR_001746709.3	n.222-12053T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308298	ENST00000833041.1	n.353-12053T>A		intron_variant	Intron 1 of 3
ENSG00000308298	ENST00000833042.1	n.177-12053T>A		intron_variant	Intron 1 of 3
ENSG00000308298	ENST00000833043.1	n.221-12053T>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107741 AN: 151910 Hom.: 38561 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.709 AC: 107814 AN: 152028 Hom.: 38591 Cov.: 31 AF XY: 0.711 AC XY: 52821 AN XY: 74308

African (AFR) AF: 0.611 AC: 25307 AN: 41438

American (AMR) AF: 0.741 AC: 11324 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2373 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4102 AN: 5152

South Asian (SAS) AF: 0.850 AC: 4084 AN: 4806

European-Finnish (FIN) AF: 0.754 AC: 7974 AN: 10574

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50172 AN: 67996

Other (OTH) AF: 0.707 AC: 1493 AN: 2112

Alfa AF: 0.724 Hom.: 5001

Bravo AF: 0.701

Asia WGS AF: 0.838 AC: 2914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.097
DANN	Benign	0.74
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs878724; hg19: chr9-73065012;