rs1993796

Variant names:

• chr4-38642429-A-G
• rs1993796
• ENST00000436901.3:n.122-6371T>C

Variant summary

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

The ENST00000436901.3(KLF3-AS1):​n.122-6371T>C variant causes a intron 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 ENST00000436901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 2 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=-0.9).
• 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 rank	MANE	Protein	UniProt
KLF3-AS1	NR_026804.1	n.454-6371T>C		intron_variant	Intron 1 of 7
KLF3-AS1	NR_171644.1	n.101-6371T>C		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF3-AS1	ENST00000436901.3	n.122-6371T>C		intron_variant	Intron 1 of 3	2
KLF3-AS1	ENST00000440181.6	n.454-6371T>C		intron_variant	Intron 1 of 7	2
KLF3-AS1	ENST00000504219.3	n.115-6371T>C		intron_variant	Intron 1 of 6	3

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

African (AFR) AF: 0.131 AC: 5441 AN: 41520

American (AMR) AF: 0.148 AC: 2263 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0256 AC: 89 AN: 3470

East Asian (EAS) AF: 0.190 AC: 983 AN: 5172

South Asian (SAS) AF: 0.164 AC: 790 AN: 4810

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00543 AC: 369 AN: 67992

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0352 Hom.: 504

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
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1993796; hg19: chr4-38644050;