chr6-43320155-T-C

Position:

• chr6-43320155-T-C

Variant summary

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

The ENST00000605935.5(ZNF318):​c.*78-1686A>G variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF318	ENST00000605935.5	c.*78-1686A>G		intron_variant, NMD_transcript_variant		1		ENSP00000475748
ZNF318	ENST00000607252.5	n.160-1686A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.889

Alfa AF: 0.887 Hom.: 75274

Bravo AF: 0.870

Asia WGS AF: 0.928 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4714675; hg19: chr6-43287893;