rs1563788

Variant names:

• chr6-43340625-C-T
• rs1563788
• NM_014345.3:c.3496-123G>A

Variant summary

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

The NM_014345.3(ZNF318):​c.3496-123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,503,926 control chromosomes in the GnomAD database, including 82,663 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 0.41 (15072 hom., cov: 32)
  • Exomes 𝑓: 0.31 (67591 hom.)
• Consequence: ZNF318 NM_014345.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 37 publications found

Genes affected

ZNF318 (HGNC:13578): (zinc finger protein 318) Predicted to enable protein heterodimerization activity and protein homodimerization activity. Predicted to be involved in negative regulation of transcription, DNA-templated and positive regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF318	NM_014345.3	c.3496-123G>A		intron_variant	Intron 9 of 9	ENST00000361428.3	NP_055160.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF318	ENST00000361428.3	c.3496-123G>A		intron_variant	Intron 9 of 9	1	NM_014345.3	ENSP00000354964.2
ZNF318	ENST00000605935.5	n.3276+2051G>A		intron_variant	Intron 7 of 9	1		ENSP00000475748.1
ZNF318	ENST00000606599.1	c.159+2051G>A		intron_variant	Intron 1 of 1	2		ENSP00000475511.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62832 AN: 151992 Hom.: 15045 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.422

GnomAD4 exome AF: 0.308 AC: 416677 AN: 1351816 Hom.: 67591 Cov.: 27 AF XY: 0.310 AC XY: 206019 AN XY: 664262

African (AFR) AF: 0.690 AC: 20305 AN: 29436

American (AMR) AF: 0.402 AC: 10828 AN: 26918

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 7203 AN: 20304

East Asian (EAS) AF: 0.328 AC: 12276 AN: 37406

South Asian (SAS) AF: 0.387 AC: 26268 AN: 67812

European-Finnish (FIN) AF: 0.276 AC: 12468 AN: 45130

Middle Eastern (MID) AF: 0.471 AC: 2420 AN: 5134

European-Non Finnish (NFE) AF: 0.287 AC: 305775 AN: 1063798

Other (OTH) AF: 0.342 AC: 19134 AN: 55878

GnomAD4 genome AF: 0.414 AC: 62915 AN: 152110 Hom.: 15072 Cov.: 32 AF XY: 0.410 AC XY: 30521 AN XY: 74372

African (AFR) AF: 0.669 AC: 27747 AN: 41490

American (AMR) AF: 0.382 AC: 5838 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1293 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1733 AN: 5186

South Asian (SAS) AF: 0.403 AC: 1943 AN: 4826

European-Finnish (FIN) AF: 0.267 AC: 2817 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20358 AN: 67980

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.354 Hom.: 2629

Bravo AF: 0.432

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.047
DANN	Benign	0.50
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs1563788; hg19: chr6-43308363; COSMIC: COSV58938183;