chrX-75369282-C-T

Position:

• chrX-75369282-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144969.3(ZDHHC15):​c.*3696G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (17700 hom., 19756 hem., cov: 22)
  • Exomes 𝑓: 0.57 (1 hom. 2 hem.)
  • Failed GnomAD Quality Control
• Consequence: ZDHHC15 NM_144969.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

Genes affected

ZDHHC15 (HGNC:20342): (zinc finger DHHC-type palmitoyltransferase 15) The protein encoded by this gene belongs to the DHHC palmitoyltransferase family. Mutations in this gene are associated with mental retardatio X-linked type 91 (MRX91). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC15	NM_144969.3	c.*3696G>A		3_prime_UTR_variant	12/12	ENST00000373367.8	NP_659406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC15	ENST00000373367.8	c.*3696G>A		3_prime_UTR_variant	12/12	1	NM_144969.3	ENSP00000362465	P1
ZDHHC15	ENST00000541184.1	c.*3696G>A		3_prime_UTR_variant	11/11	2		ENSP00000445420

Frequencies

GnomAD3 genomes AF: 0.633 AC: 68381 AN: 107989 Hom.: 17714 Cov.: 22 AF XY: 0.650 AC XY: 19736 AN XY: 30381

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.688

GnomAD4 exome AF: 0.571 AC: 4 AN: 7 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 2 AN XY: 3

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.633 AC: 68370 AN: 108040 Hom.: 17700 Cov.: 22 AF XY: 0.649 AC XY: 19756 AN XY: 30442

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.680

Alfa AF: 0.740 Hom.: 21252

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.25

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

LitVar

Other links and lift over

dbSNP: rs7052314; hg19: chrX-74589117;