rs191757590

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-814800-G-A
• chr5-814800-G-C
• chr5-814800-G-T

Variant summary

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

The NM_024786.3(ZDHHC11):​c.1147-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000504 in 1,387,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000050 (0 hom.)
• Consequence: ZDHHC11 NM_024786.3 splice_region, intron
• Scores: Splicing: ADA: 0.00001460
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000504 AC: 7 AN: 1387716 Hom.: 0 Cov.: 30 AF XY: 0.00000436 AC XY: 3 AN XY: 687706

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: 0.00000651

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
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000015
dbscSNV1_RF	Benign	0.020
SpliceAI score (max)		0.020		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: chr5-814915;