rs963265

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-70479619-T-A
• chr9-70479619-T-C
• chr9-70479619-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000833041.1(ENSG00000308298):​n.520+16764T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000308298 ENST00000833041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

Genes affected

ENSG00000308298 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF9-DT	XR_001746707.3	n.390-15015T>A		intron_variant	Intron 3 of 4
KLF9-DT	XR_001746708.3	n.390-15015T>A		intron_variant	Intron 3 of 4
KLF9-DT	XR_001746709.3	n.389+16764T>A		intron_variant	Intron 3 of 3
KLF9-DT	XR_001746710.3	n.389+16764T>A		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>A		intron_variant	Intron 3 of 3
ENSG00000308298	ENST00000833042.1	n.344+16764T>A		intron_variant	Intron 3 of 3
ENSG00000308298	ENST00000833043.1	n.388+16764T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.38
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;