rs337629

chr4-38633737-A-Gchr4-38633737-A-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.203+2219T>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 0.828 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 NR_171644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

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=-0.91).
• 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/exons	MANE	UniProt
KLF3-AS1	NR_171644.1	n.203+2219T>C		intron_variant, non_coding_transcript_variant
KLF3-AS1	NR_026804.1	n.556+2219T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF3-AS1	ENST00000655930.1	n.159+2219T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.963

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.781

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337629; hg19: chr4-38635358;