6-43320155-T-C

Variant names:

• chr6-43320155-T-C
• rs4714675
• ENST00000605935.5:n.*78-1686A>G

Variant summary

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

The ENST00000605935.5(ZNF318):​n.*78-1686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,304 control chromosomes in the GnomAD database, including 58,639 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 0.88 (58639 hom., cov: 32)
• Consequence: ZNF318 ENST00000605935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605935.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF318	ENST00000605935.5	TSL:1	n.*78-1686A>G		intron	N/A	ENSP00000475748.1	Q5VUA4-2
	ZNF318	ENST00000607252.5	TSL:1	n.160-1686A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133354 AN: 152186 Hom.: 58611 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.876 AC: 133424 AN: 152304 Hom.: 58639 Cov.: 32 AF XY: 0.878 AC XY: 65421 AN XY: 74480

African (AFR) AF: 0.816 AC: 33900 AN: 41554

American (AMR) AF: 0.866 AC: 13252 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3226 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5165 AN: 5184

South Asian (SAS) AF: 0.913 AC: 4411 AN: 4832

European-Finnish (FIN) AF: 0.928 AC: 9855 AN: 10616

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60590 AN: 68020

Other (OTH) AF: 0.889 AC: 1879 AN: 2114

Alfa AF: 0.885 Hom.: 95976

Bravo AF: 0.870

Asia WGS AF: 0.928 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4714675;

hg19: chr6-43287893;