NM_024786.3:c.1147-5C>A

Variant names:

• chr5-814800-G-T
• rs191757590
• NM_024786.3:c.1147-5C>A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_024786.3(ZDHHC11):​c.1147-5C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 1,539,072 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00020 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00024 (11 hom.)
• Consequence: ZDHHC11 NM_024786.3 splice_region, intron
• Scores: Splicing: ADA: 0.00002018
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

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 Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAdExome4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC11	NM_024786.3	c.1147-5C>A		splice_region_variant, intron_variant	Intron 10 of 12	ENST00000283441.13	NP_079062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC11	ENST00000283441.13	c.1147-5C>A		splice_region_variant, intron_variant	Intron 10 of 12	1	NM_024786.3	ENSP00000283441.8
ZDHHC11	ENST00000503758.6	n.2849-5C>A		splice_region_variant, intron_variant	Intron 9 of 11	5
ZDHHC11	ENST00000507800.1	n.*769-5C>A		splice_region_variant, intron_variant	Intron 9 of 11	5		ENSP00000423817.1

Frequencies

GnomAD3 genomes AF: 0.000212 AC: 32 AN: 151246 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.0000971

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000658

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000836

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000237

Gnomad OTH AF: 0.00145

GnomAD3 exomes AF: 0.000273 AC: 54 AN: 197598 Hom.: 1 AF XY: 0.000316 AC XY: 34 AN XY: 107622

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.000503

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000389

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000390

Gnomad OTH exome AF: 0.000451

GnomAD4 exome AF: 0.000241 AC: 334 AN: 1387708 Hom.: 11 Cov.: 30 AF XY: 0.000246 AC XY: 169 AN XY: 687700

Gnomad4 AFR exome AF: 0.000129

Gnomad4 AMR exome AF: 0.000222

Gnomad4 ASJ exome AF: 0.000874

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000679

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000154

Gnomad4 OTH exome AF: 0.000262

GnomAD4 genome AF: 0.000205 AC: 31 AN: 151364 Hom.: 1 Cov.: 33 AF XY: 0.000203 AC XY: 15 AN XY: 73974

Gnomad4 AFR AF: 0.0000968

Gnomad4 AMR AF: 0.0000657

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000837

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000237

Gnomad4 OTH AF: 0.00143

Alfa AF: 0.000395 Hom.: 1

Bravo AF: 0.000196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000020
dbscSNV1_RF	Benign	0.026
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs191757590; hg19: chr5-814915;