ENST00000532699.1:n.315-6154C>G

Variant names:

• chr11-112082853-A-G
• NM_018195.4:c.763A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_018195.4(NKAPD1):​c.763A>G​(p.Arg255Gly) variant causes a missense 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. 12/18 in silico tools predict 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)
• Consequence: NKAPD1 NM_018195.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08411673).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAPD1	NM_018195.4	c.763A>G	p.Arg255Gly	missense_variant	Exon 6 of 6	ENST00000393047.8	NP_060665.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAPD1	ENST00000393047.8	c.763A>G	p.Arg255Gly	missense_variant	Exon 6 of 6	1	NM_018195.4	ENSP00000376767.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.065	T;.;T;.
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.75	.;T;T;T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.084	T;T;T;T
MetaSVM	Benign	-1.1	T
PROVEAN	Benign	-1.7	N;N;N;N
REVEL	Benign	0.054
Sift	Uncertain	0.0080	D;D;D;D
Sift4G	Uncertain	0.042	D;D;D;D
Polyphen		0.0	B;.;B;B
Vest4		0.081
MutPred		0.24		Gain of loop (P = 0.0045);.;Gain of loop (P = 0.0045);.;
MVP		0.082
MPC		0.25
ClinPred		0.28	T
GERP RS		3.4
Varity_R		0.089
gMVP		0.13

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-111953577;