rs878724

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833041.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308298	ENST00000833041.1		n.353-12053T>A		intron	N/A
	ENSG00000308298	ENST00000833042.1		n.177-12053T>A		intron	N/A
	ENSG00000308298	ENST00000833043.1		n.221-12053T>A		intron	N/A

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 v4.9

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;