chr9-70479619-T-C

Variant names:

• chr9-70479619-T-C
• rs963265
• ENST00000833041.1:n.520+16764T>C

Variant summary

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

The ENST00000833041.1(ENSG00000308298):​n.520+16764T>C variant causes a intron 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: ENSG00000308298 ENST00000833041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 10 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=-0.85).
• 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 rank	MANE	Protein	UniProt
KLF9-DT	XR_001746707.3	n.390-15015T>C		intron_variant	Intron 3 of 4
KLF9-DT	XR_001746708.3	n.390-15015T>C		intron_variant	Intron 3 of 4
KLF9-DT	XR_001746709.3	n.389+16764T>C		intron_variant	Intron 3 of 3
KLF9-DT	XR_001746710.3	n.389+16764T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308298	ENST00000833041.1	n.520+16764T>C		intron_variant	Intron 3 of 3
ENSG00000308298	ENST00000833042.1	n.344+16764T>C		intron_variant	Intron 3 of 3
ENSG00000308298	ENST00000833043.1	n.388+16764T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.249 AC: 10000 AN: 40236

American (AMR) AF: 0.433 AC: 6605 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1257 AN: 3466

East Asian (EAS) AF: 0.163 AC: 844 AN: 5172

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4826

European-Finnish (FIN) AF: 0.336 AC: 3554 AN: 10574

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29136 AN: 67944

Other (OTH) AF: 0.360 AC: 760 AN: 2110

Alfa AF: 0.398 Hom.: 3030

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs963265; hg19: chr9-73094535;