rs1993796

chr4-38642429-A-G

Variant summary

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

The NR_171644.1(KLF3-AS1):n.101-6371T>C 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 0.0662 in 152,188 control chromosomes in the GnomAD database, including 761 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 0.066 (761 hom., cov: 32)
• Consequence: KLF3-AS1 NR_171644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF3-AS1	NR_171644.1	n.101-6371T>C		intron_variant, non_coding_transcript_variant
KLF3-AS1	NR_026804.1	n.454-6371T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF3-AS1	ENST00000655930.1	n.57-6371T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10054 AN: 152070 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00543

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0662 AC: 10069 AN: 152188 Hom.: 761 Cov.: 32 AF XY: 0.0701 AC XY: 5213 AN XY: 74414

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0256

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00543

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0282 Hom.: 327

Bravo AF: 0.0797

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993796; hg19: chr4-38644050;