NM_024786.3:c.1169T>A

Variant names:

• chr5-814773-A-T
• NM_024786.3:c.1169T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024786.3(ZDHHC11):​c.1169T>A​(p.Ile390Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000714 in 1,401,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. I390M) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000071 (0 hom.)
• Consequence: ZDHHC11 NM_024786.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ZDHHC11 (HGNC:19158): (zinc finger DHHC-type containing 11) Enables signaling adaptor activity. Involved in antiviral innate immune response and positive regulation of defense response to virus by host. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.051211566).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC11	NM_024786.3	c.1169T>A	p.Ile390Lys	missense_variant	Exon 11 of 13	ENST00000283441.13	NP_079062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC11	ENST00000283441.13	c.1169T>A	p.Ile390Lys	missense_variant	Exon 11 of 13	1	NM_024786.3	ENSP00000283441.8
ZDHHC11	ENST00000503758.6	n.2871T>A		non_coding_transcript_exon_variant	Exon 10 of 12	5
ZDHHC11	ENST00000507800.1	n.*791T>A		non_coding_transcript_exon_variant	Exon 10 of 12	5		ENSP00000423817.1
ZDHHC11	ENST00000507800.1	n.*791T>A		3_prime_UTR_variant	Exon 10 of 12	5		ENSP00000423817.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000714 AC: 10 AN: 1401472 Hom.: 0 Cov.: 30 AF XY: 0.00000720 AC XY: 5 AN XY: 694762

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000925

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.29
DANN	Benign	0.54
DEOGEN2	Benign	0.0012	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.0061	N
LIST_S2	Benign	0.18	T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.051	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PrimateAI	Benign	0.29	T
PROVEAN	Benign	0.050	N
REVEL	Benign	0.010
Sift	Uncertain	0.014	D
Sift4G	Benign	0.10	T
Polyphen		0.0	B
Vest4		0.099
MutPred		0.26		Gain of ubiquitination at I390 (P = 0.0014);
MVP		0.15
MPC		0.098
ClinPred		0.062	T
GERP RS		0.24
Varity_R		0.037
gMVP		0.044

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr5-814888;