rs1602459

Variant names:

• chr4-38640548-G-A
• rs1602459
• ENST00000436901.3:n.122-4490C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-38640548-G-A
• chr4-38640548-G-T

Variant summary

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

The ENST00000436901.3(KLF3-AS1):​n.122-4490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 150,908 control chromosomes in the GnomAD database, including 751 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 0.067 (751 hom., cov: 32)
• Consequence: KLF3-AS1 ENST00000436901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF3-AS1	NR_026804.1	n.454-4490C>T		intron_variant	Intron 1 of 7
KLF3-AS1	NR_171644.1	n.101-4490C>T		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF3-AS1	ENST00000436901.3	n.122-4490C>T		intron_variant	Intron 1 of 3	2
KLF3-AS1	ENST00000440181.6	n.454-4490C>T		intron_variant	Intron 1 of 7	2
KLF3-AS1	ENST00000504219.3	n.115-4490C>T		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10021 AN: 150790 Hom.: 749 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.000489

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00544

Gnomad OTH AF: 0.0571

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

GnomAD4 genome AF: 0.0665 AC: 10036 AN: 150908 Hom.: 751 Cov.: 32 AF XY: 0.0706 AC XY: 5197 AN XY: 73652

African (AFR) AF: 0.132 AC: 5414 AN: 41048

American (AMR) AF: 0.149 AC: 2259 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3460

East Asian (EAS) AF: 0.191 AC: 981 AN: 5136

South Asian (SAS) AF: 0.165 AC: 791 AN: 4784

European-Finnish (FIN) AF: 0.000489 AC: 5 AN: 10218

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.00544 AC: 369 AN: 67808

Other (OTH) AF: 0.0598 AC: 125 AN: 2090

Alfa AF: 0.0365 Hom.: 55

Bravo AF: 0.0798

Asia WGS AF: 0.176 AC: 613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1602459; hg19: chr4-38642169;