rs150354646

Variant names:

• chr5-850572-C-A
• rs150354646
• NM_024786.3:c.31G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-850572-C-A
• chr5-850572-C-G
• chr5-850572-C-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_024786.3(ZDHHC11):​c.31G>T​(p.Val11Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,613,458 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0088 (24 hom., cov: 33)
  • Exomes 𝑓: 0.00093 (18 hom.)
• Consequence: ZDHHC11 NM_024786.3 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.640
• Publications: 0 publications found

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]

BRD9 (HGNC:25818): (bromodomain containing 9) Enables lysine-acetylated histone binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of SWI/SNF complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.002983898).
• BP6: Variant 5-850572-C-A is Benign according to our data. Variant chr5-850572-C-A is described in ClinVar as Benign. ClinVar VariationId is 784048.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00876 (1333/152218) while in subpopulation AFR AF = 0.0302 (1254/41530). AF 95% confidence interval is 0.0288. There are 24 homozygotes in GnomAd4. There are 605 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 24 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024786.3. 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
	ZDHHC11	NM_024786.3	MANE Select	c.31G>T	p.Val11Phe	missense	Exon 1 of 13	NP_079062.1	Q9H8X9-1
	ZDHHC11	NM_001393492.1		c.31G>T	p.Val11Phe	missense	Exon 1 of 13	NP_001380421.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC11	ENST00000283441.13	TSL:1 MANE Select	c.31G>T	p.Val11Phe	missense	Exon 1 of 13	ENSP00000283441.8	Q9H8X9-1
	ZDHHC11	ENST00000685990.1		c.31G>T	p.Val11Phe	missense	Exon 2 of 4	ENSP00000509570.1	A0A8I5KQG6
	BRD9	ENST00000493082.5	TSL:5	n.469G>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.00877 AC: 1334 AN: 152100 Hom.: 24 Cov.: 33

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00340

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00480

GnomAD2 exomes AF: 0.00234 AC: 588 AN: 251278 AF XY: 0.00169

Gnomad AFR exome AF: 0.0311

Gnomad AMR exome AF: 0.00139

Gnomad ASJ exome AF: 0.00149

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000106

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.000928 AC: 1356 AN: 1461240 Hom.: 18 Cov.: 31 AF XY: 0.000784 AC XY: 570 AN XY: 726948

African (AFR) AF: 0.0297 AC: 995 AN: 33480

American (AMR) AF: 0.00168 AC: 75 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00184 AC: 48 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000348 AC: 3 AN: 86254

European-Finnish (FIN) AF: 0.0000189 AC: 1 AN: 52808

Middle Eastern (MID) AF: 0.000867 AC: 5 AN: 5764

European-Non Finnish (NFE) AF: 0.0000899 AC: 100 AN: 1111998

Other (OTH) AF: 0.00214 AC: 129 AN: 60384

GnomAD4 genome AF: 0.00876 AC: 1333 AN: 152218 Hom.: 24 Cov.: 33 AF XY: 0.00813 AC XY: 605 AN XY: 74432

African (AFR) AF: 0.0302 AC: 1254 AN: 41530

American (AMR) AF: 0.00340 AC: 52 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 67998

Other (OTH) AF: 0.00475 AC: 10 AN: 2106

Alfa AF: 0.00261 Hom.: 2

Bravo AF: 0.0102

ESP6500AA AF: 0.0325 AC: 143

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.00287 AC: 348

Asia WGS AF: 0.00115 AC: 4 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.000178

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.57	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.6
DANN	Uncertain	0.98
DEOGEN2	Benign	0.012	T
Eigen	Benign	-0.89
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.087	N
LIST_S2	Benign	0.40	T
MetaRNN	Benign	0.0030	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.64
PrimateAI	Benign	0.46	T
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.011
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0020	D
Polyphen		0.45	B
Vest4		0.19
MVP		0.25
MPC		0.076
ClinPred		0.044	T
GERP RS		0.27
PromoterAI		-0.019	Neutral
Varity_R		0.20
gMVP		0.51
Mutation Taster		=99/1	polymorphism

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

dbSNP: rs150354646; hg19: chr5-850687;