rs4833079

Variant names:

• chr4-38653060-T-C
• rs4833079
• ENST00000436901.3:n.121+11734A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

KLF3-AS1 (HGNC:25796): (KLF3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436901.3. 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
	KLF3-AS1	NR_026804.1		n.453+11116A>G		intron	N/A
	KLF3-AS1	NR_171644.1		n.100+11734A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF3-AS1	ENST00000436901.3	TSL:2	n.121+11734A>G		intron	N/A
	KLF3-AS1	ENST00000440181.6	TSL:2	n.453+11116A>G		intron	N/A
	KLF3-AS1	ENST00000504219.3	TSL:3	n.114+11734A>G		intron	N/A

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

African (AFR) AF: 0.158 AC: 6553 AN: 41514

American (AMR) AF: 0.227 AC: 3477 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5188

South Asian (SAS) AF: 0.111 AC: 534 AN: 4826

European-Finnish (FIN) AF: 0.485 AC: 5133 AN: 10574

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27215 AN: 68002

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.351 Hom.: 15468

Bravo AF: 0.270

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.73
DANN	Benign	0.60
PhyloP100		-0.099

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4833079;

hg19: chr4-38654681;