1-44088785-C-T

Variant names:

• chr1-44088785-C-T
• rs6698333
• ENST00000434244.5:n.931-12775C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434244.5(ENSG00000230615):​n.931-12775C>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: ENSG00000230615 ENST00000434244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434244.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230615	ENST00000434244.5	TSL:1	n.931-12775C>T		intron	N/A
	ENSG00000230615	ENST00000616338.2	TSL:4	n.397-12775C>T		intron	N/A
	ENSG00000230615	ENST00000836620.1		n.1007-12775C>T		intron	N/A

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

African (AFR) AF: 0.515 AC: 21321 AN: 41408

American (AMR) AF: 0.531 AC: 8107 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2321 AN: 5146

South Asian (SAS) AF: 0.458 AC: 2202 AN: 4810

European-Finnish (FIN) AF: 0.483 AC: 5083 AN: 10526

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29669 AN: 67930

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.444 Hom.: 30960

Bravo AF: 0.476

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.49
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6698333; hg19: chr1-44554457;