rs9317757

Variant names:

• chr13-68986297-C-T
• rs9317757

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.163 in 152,072 control chromosomes in the GnomAD database, including 2,106 homozygotes. 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 0.16 (2106 hom., cov: 33)
• Consequence: ZDHHC20P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 5 publications found

Genes affected

ZDHHC20P4 (HGNC:39776): (zinc finger DHHC-type containing 20 pseudogene 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC20P4		n.68986297C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P4	ENST00000411421.1	n.*233C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24834 AN: 151954 Hom.: 2109 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24821 AN: 152072 Hom.: 2106 Cov.: 33 AF XY: 0.164 AC XY: 12177 AN XY: 74358

African (AFR) AF: 0.163 AC: 6751 AN: 41470

American (AMR) AF: 0.122 AC: 1864 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3470

East Asian (EAS) AF: 0.129 AC: 670 AN: 5178

South Asian (SAS) AF: 0.172 AC: 828 AN: 4824

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10550

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11744 AN: 67978

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.167 Hom.: 795

Bravo AF: 0.155

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.4
DANN	Benign	0.47
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9317757; hg19: chr13-69560429;