chr9-70503748-G-T

Variant names:

• chr9-70503748-G-T
• rs10868841
• ENST00000833041.1:n.520+40893G>T

Variant summary

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

The ENST00000833041.1(ENSG00000308298):​n.520+40893G>T variant causes a intron 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: ENSG00000308298 ENST00000833041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 5 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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 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.520+40893G>T		intron	N/A
	ENSG00000308298	ENST00000833042.1		n.344+40893G>T		intron	N/A
	ENSG00000308298	ENST00000833043.1		n.388+40893G>T		intron	N/A

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

African (AFR) AF: 0.100 AC: 4163 AN: 41520

American (AMR) AF: 0.314 AC: 4801 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 931 AN: 3464

East Asian (EAS) AF: 0.490 AC: 2520 AN: 5148

South Asian (SAS) AF: 0.206 AC: 993 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4911 AN: 10546

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23857 AN: 67968

Other (OTH) AF: 0.284 AC: 600 AN: 2112

Alfa AF: 0.318 Hom.: 5604

Bravo AF: 0.271

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10868841; hg19: chr9-73118664;