19-1864602-C-T

Variant names:

• chr19-1864602-C-T
• rs3810417
• ENST00000789288.1:n.233+193C>T

Variant summary

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

The ENST00000789288.1(ENSG00000302738):​n.233+193C>T 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: ENSG00000302738 ENST00000789288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 9 publications found

Genes affected

ENSG00000302738 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KLF16	XM_047439498.1	c.428-9842G>A		intron_variant	Intron 1 of 1		XP_047295454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302738	ENST00000789288.1	n.233+193C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.422 AC: 17512 AN: 41454

American (AMR) AF: 0.328 AC: 5015 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 529 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2106 AN: 10596

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11568 AN: 67978

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.200 Hom.: 5378

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs3810417; hg19: chr19-1864601;