1-44088785-C-T

Position:

• chr1-44088785-C-T

Variant summary

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

The XM_011540700.2(KLF17):​c.-31+37291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,868 control chromosomes in the GnomAD database, including 17,054 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 0.47 (17054 hom., cov: 31)
• Consequence: KLF17 XM_011540700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

ENSG00000230615 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF17	XM_011540700.2	c.-31+37291C>T		intron_variant			XP_011539002.1
KLF17	XM_047445936.1	c.-31+37254C>T		intron_variant			XP_047301892.1
KLF17	XM_047445938.1	c.-31+37254C>T		intron_variant			XP_047301894.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230615	ENST00000434244.5	n.931-12775C>T		intron_variant		1
ENSG00000230615	ENST00000616338.2	n.397-12775C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71319 AN: 151748 Hom.: 17030 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.470 AC: 71401 AN: 151868 Hom.: 17054 Cov.: 31 AF XY: 0.474 AC XY: 35191 AN XY: 74212

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.456

Alfa AF: 0.440 Hom.: 22212

Bravo AF: 0.476

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6698333; hg19: chr1-44554457;