rs4833079

Positions:

• chr4-38653060-T-C

Variant summary

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

The ENST00000436901.3(KLF3-AS1):​n.121+11734A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,174 control chromosomes in the GnomAD database, including 7,940 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 0.29 (7940 hom., cov: 32)
• Consequence: KLF3-AS1 ENST00000436901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

KLF3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF3-AS1	NR_026804.1	n.453+11116A>G		intron_variant
KLF3-AS1	NR_171644.1	n.100+11734A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF3-AS1	ENST00000436901.3	n.121+11734A>G		intron_variant		2
KLF3-AS1	ENST00000440181.6	n.453+11116A>G		intron_variant		2
KLF3-AS1	ENST00000504219.2	n.100+11734A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44797 AN: 152056 Hom.: 7942 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.294 AC: 44801 AN: 152174 Hom.: 7940 Cov.: 32 AF XY: 0.291 AC XY: 21668 AN XY: 74412

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.267

Alfa AF: 0.354 Hom.: 10794

Bravo AF: 0.270

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.73
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833079; hg19: chr4-38654681;