rs1408919

Positions:

• chr1-44105456-A-G

Variant summary

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

The XM_011540700.2(KLF17):​c.-30-23897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,808 control chromosomes in the GnomAD database, including 6,630 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 0.29 (6628 hom., cov: 31)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: KLF17 XM_011540700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

KLF17 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF17	XM_011540700.2	c.-30-23897A>G		intron_variant
KLF17	XM_047445936.1	c.-30-23897A>G		intron_variant
KLF17	XM_047445938.1	c.-30-23897A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000625367.2	n.308A>G		non_coding_transcript_exon_variant	2/3	5
	ENST00000627824.2	n.633A>G		non_coding_transcript_exon_variant	2/3	5
	ENST00000627999.1	n.224A>G		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43904 AN: 151684 Hom.: 6624 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 2 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.289 AC: 43929 AN: 151788 Hom.: 6628 Cov.: 31 AF XY: 0.292 AC XY: 21634 AN XY: 74150

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.317

Alfa AF: 0.309 Hom.: 1486

Bravo AF: 0.286

Asia WGS AF: 0.327 AC: 1139 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	5.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408919; hg19: chr1-44571128;