Genetic Variant ENST00000532699.1:n.315-6154C>A (chr11-112082853-A-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACMG Germline Pathogenicity v2019). PM2

The NM_018195.4(NKAPD1):c. variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

NKAPD1
NM_018195.4 exon_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

Publications

0 publications found

Variant links:

Genes affected

NKAPD1 (HGNC:25569): (NKAP domain containing 1) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Jul 2025]

NKAPD1 links:

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new If you want to explore the variant's impact on the transcript NM_018195.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_018195.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
NKAPD1 NM_018195.4	MANE Select	c.	exon_region	Exon 6 of 6	Prot: NP_060665.3
NKAPD1 NM_018195.4	MANE Select	c.	3_prime_UTR	Exon 6 of 6	Prot: NP_060665.3
NKAPD1 NM_001082969.2		c.	exon_region	Exon 6 of 6	Prot: NP_001076438.1 UniProt: Q6ZUT1-2

NKAPD1 NM_018195.4

MANE Select

HGVSc / HGVSpc.

Exon rankExon 6 of 6

exon_region

Prot: NP_060665.3

NKAPD1 NM_018195.4

MANE Select

HGVSc / HGVSpc.

Exon rankExon 6 of 6

3_prime_UTR

Prot: NP_060665.3

NKAPD1 NM_001082969.2

HGVSc / HGVSpc.

Exon rankExon 6 of 6

exon_region

Prot: NP_001076438.1UniProt: Q6ZUT1-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NKAPD1 ENST00000525785.5	TSL:5	c.	downstream_gene	N/A	Prot: ENSP00000435408.1 UniProt: E9PKA8

NKAPD1 ENST00000525785.5

TSL:5

HGVSc / HGVSpc.

Exon rankN/A

downstream_gene

Prot: ENSP00000435408.1UniProt: E9PKA8

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	-0.015

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence