6-43312975-C-T

Variant names:

• chr6-43312975-C-T
• rs10948071
• ENST00000605935.5:n.*246-1719G>A

Variant summary

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

The ENST00000605935.5(ZNF318):​n.*246-1719G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,684 control chromosomes in the GnomAD database, including 19,485 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 0.46 (19485 hom., cov: 35)
• Consequence: ZNF318 ENST00000605935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 18 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF318	ENST00000605935.5	n.*246-1719G>A		intron_variant	Intron 9 of 9	1		ENSP00000475748.1
ZNF318	ENST00000607252.5	n.328-4566G>A		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70500 AN: 151566 Hom.: 19496 Cov.: 35

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.465 AC: 70486 AN: 151684 Hom.: 19485 Cov.: 35 AF XY: 0.470 AC XY: 34864 AN XY: 74118

African (AFR) AF: 0.150 AC: 6227 AN: 41446

American (AMR) AF: 0.487 AC: 7414 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1941 AN: 3454

East Asian (EAS) AF: 0.663 AC: 3390 AN: 5116

South Asian (SAS) AF: 0.517 AC: 2483 AN: 4800

European-Finnish (FIN) AF: 0.661 AC: 6964 AN: 10530

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40235 AN: 67816

Other (OTH) AF: 0.470 AC: 986 AN: 2100

Alfa AF: 0.493 Hom.: 2383

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.42
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10948071; hg19: chr6-43280713;