19-1854723-GTC-ATT

Variant names:

• chr19-1854723-GTC-ATT
• NM_031918.4:c.493_495delGACinsAAT
• KLF16 p.Asp165Asn

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_031918.4(KLF16):​c.493_495delGACinsAAT​(p.Asp165Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D165H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KLF16 NM_031918.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031918.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF16	NM_031918.4	MANE Select	c.493_495delGACinsAAT	p.Asp165Asn	missense	N/A	NP_114124.1	Q9BXK1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF16	ENST00000250916.6	TSL:1 MANE Select	c.493_495delGACinsAAT	p.Asp165Asn	missense	N/A	ENSP00000250916.3	Q9BXK1
	KLF16	ENST00000617223.1	TSL:1	c.493_495delGACinsAAT	p.Asp165Asn	missense	N/A	ENSP00000483701.1	Q9BXK1
	KLF16	ENST00000541015.5	TSL:1	n.493_495delGACinsAAT		non_coding_transcript_exon	Exon 2 of 3	ENSP00000439973.1	Q9BXK1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-1854722;