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:18830): (KLF transcription factor 17) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within gamete generation. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230615 (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	Protein	UniProt
KLF17	XM_011540700.2	c.-30-23897A>G		intron_variant			XP_011539002.1
KLF17	XM_047445936.1	c.-30-23897A>G		intron_variant			XP_047301892.1
KLF17	XM_047445938.1	c.-30-23897A>G		intron_variant			XP_047301894.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230615	ENST00000625367.2	n.308A>G		non_coding_transcript_exon_variant	2/3	5
ENSG00000230615	ENST00000627824.2	n.633A>G		non_coding_transcript_exon_variant	2/3	5
ENSG00000230615	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;