ENST00000532699.1:n.315-5708C>T

Variant names:

• chr11-112083299-G-T
• NM_018195.4:c.*327G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018195.4(NKAPD1):​c.*327G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NKAPD1 NM_018195.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.843
• Publications: 0 publications found

Genes affected

NKAPD1 (HGNC:25569): (NKAP domain containing 1) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018195.4. 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
	NKAPD1	NM_018195.4	MANE Select	c.*327G>T		3_prime_UTR	Exon 6 of 6	NP_060665.3
	NKAPD1	NR_103469.2		n.1876G>T		non_coding_transcript_exon	Exon 6 of 6
	NKAPD1	NM_001082969.2		c.*327G>T		3_prime_UTR	Exon 6 of 6	NP_001076438.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAPD1	ENST00000393047.8	TSL:1 MANE Select	c.*327G>T		3_prime_UTR	Exon 6 of 6	ENSP00000376767.3
	NKAPD1	ENST00000420986.6	TSL:1	c.*327G>T		3_prime_UTR	Exon 6 of 6	ENSP00000402208.2
	NKAPD1	ENST00000280352.13	TSL:2	c.*327G>T		3_prime_UTR	Exon 6 of 6	ENSP00000339076.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 30184 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 15602

African (AFR) AF: 0.00 AC: 0 AN: 986

American (AMR) AF: 0.00 AC: 0 AN: 1940

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1182

East Asian (EAS) AF: 0.00 AC: 0 AN: 2562

South Asian (SAS) AF: 0.00 AC: 0 AN: 1028

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1228

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 132

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 19272

Other (OTH) AF: 0.00 AC: 0 AN: 1854

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.50
PhyloP100		0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr11-111954023;