19-1864602-C-T

Position:

• chr19-1864602-C-T

Variant summary

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

The XM_047439498.1(KLF16):​c.428-9842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,110 control chromosomes in the GnomAD database, including 6,208 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 0.26 (6208 hom., cov: 33)
• Consequence: KLF16 XM_047439498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

Genes affected

KLF16 (HGNC:16857): (KLF transcription factor 16) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within dopamine receptor signaling pathway. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF16	XM_047439498.1	c.428-9842G>A		intron_variant			XP_047295454.1
		n.1864602C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40099 AN: 151992 Hom.: 6197 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.264 AC: 40148 AN: 152110 Hom.: 6208 Cov.: 33 AF XY: 0.265 AC XY: 19693 AN XY: 74376

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.241

Alfa AF: 0.188 Hom.: 2902

Bravo AF: 0.281

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810417; hg19: chr19-1864601;