rs337629

Variant names:

• chr4-38633737-A-G
• rs337629
• ENST00000436901.3:n.224+2219T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-38633737-A-G
• chr4-38633737-A-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.224+2219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 151,882 control chromosomes in the GnomAD database, including 52,883 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 0.83 (52883 hom., cov: 29)
• Consequence: KLF3-AS1 ENST00000436901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF3-AS1	NR_026804.1	n.556+2219T>C		intron_variant	Intron 2 of 7
KLF3-AS1	NR_171644.1	n.203+2219T>C		intron_variant	Intron 2 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF3-AS1	ENST00000436901.3	n.224+2219T>C		intron_variant	Intron 2 of 3	2
KLF3-AS1	ENST00000440181.6	n.556+2219T>C		intron_variant	Intron 2 of 7	2
KLF3-AS1	ENST00000504219.3	n.217+2219T>C		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125652 AN: 151766 Hom.: 52817 Cov.: 29

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.828 AC: 125777 AN: 151882 Hom.: 52883 Cov.: 29 AF XY: 0.825 AC XY: 61217 AN XY: 74184

African (AFR) AF: 0.963 AC: 39947 AN: 41484

American (AMR) AF: 0.801 AC: 12211 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2532 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2764 AN: 5134

South Asian (SAS) AF: 0.784 AC: 3758 AN: 4792

European-Finnish (FIN) AF: 0.799 AC: 8410 AN: 10524

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53672 AN: 67934

Other (OTH) AF: 0.781 AC: 1636 AN: 2096

Alfa AF: 0.805 Hom.: 5813

Bravo AF: 0.832

Asia WGS AF: 0.738 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.56
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs337629; hg19: chr4-38635358;