9-70503748-G-T

Position:

• chr9-70503748-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746707.3(KLF9-DT):​n.466+9038G>T 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 0.283 in 152,062 control chromosomes in the GnomAD database, including 7,290 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 0.28 (7290 hom., cov: 32)
• Consequence: KLF9-DT XR_001746707.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

KLF9-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF9-DT	XR_001746707.3	n.466+9038G>T		intron_variant, non_coding_transcript_variant
KLF9-DT	XR_001746709.3	n.390-10818G>T		intron_variant, non_coding_transcript_variant
KLF9-DT	XR_001746710.3	n.389+40893G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43091 AN: 151944 Hom.: 7284 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.283 AC: 43098 AN: 152062 Hom.: 7290 Cov.: 32 AF XY: 0.288 AC XY: 21410 AN XY: 74316

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.284

Alfa AF: 0.301 Hom.: 3813

Bravo AF: 0.271

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10868841; hg19: chr9-73118664;