rs1602459

chr4-38640548-G-Achr4-38640548-G-T

Variant summary

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

The NR_171644.1(KLF3-AS1):n.101-4490C>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 0.0665 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 NR_171644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KLF3-AS1	NR_171644.1	n.101-4490C>T		intron_variant, non_coding_transcript_variant
KLF3-AS1	NR_026804.1	n.454-4490C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF3-AS1	ENST00000655930.1	n.57-4490C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.000489

Gnomad4 NFE AF: 0.00544

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.0323 Hom.: 47

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1602459; hg19: chr4-38642169;