19-52880932-C-T

Variant names:

• chr19-52880932-C-T
• rs6509701
• NM_001351774.2:c.1194G>A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001351774.2(ZNF320):​c.1194G>A​(p.Ala398Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 1,613,686 control chromosomes in the GnomAD database, including 374,867 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 0.66 (33412 hom., cov: 32)
  • Exomes 𝑓: 0.68 (341455 hom.)
• Consequence: ZNF320 NM_001351774.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60

Genes affected

ZNF320 (HGNC:13842): (zinc finger protein 320) ZNF320 encodes a Kruppel-like zinc finger protein. Members of this protein family are involved in activation or repression of transcription.[supplied by OMIM, Jul 2002]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=-3.6 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF320	NM_001351774.2	c.1194G>A	p.Ala398Ala	synonymous_variant	Exon 6 of 6	ENST00000682928.1	NP_001338703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF320	ENST00000682928.1	c.1194G>A	p.Ala398Ala	synonymous_variant	Exon 6 of 6		NM_001351774.2	ENSP00000506814.1

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99905 AN: 151802 Hom.: 33397 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.633

GnomAD3 exomes AF: 0.620 AC: 155639 AN: 251208 Hom.: 50418 AF XY: 0.631 AC XY: 85642 AN XY: 135766

Gnomad AFR exome AF: 0.678

Gnomad AMR exome AF: 0.389

Gnomad ASJ exome AF: 0.676

Gnomad EAS exome AF: 0.376

Gnomad SAS exome AF: 0.633

Gnomad FIN exome AF: 0.708

Gnomad NFE exome AF: 0.694

Gnomad OTH exome AF: 0.642

GnomAD4 exome AF: 0.679 AC: 992680 AN: 1461764 Hom.: 341455 Cov.: 64 AF XY: 0.679 AC XY: 493402 AN XY: 727182

Gnomad4 AFR exome AF: 0.679

Gnomad4 AMR exome AF: 0.408

Gnomad4 ASJ exome AF: 0.678

Gnomad4 EAS exome AF: 0.410

Gnomad4 SAS exome AF: 0.634

Gnomad4 FIN exome AF: 0.707

Gnomad4 NFE exome AF: 0.703

Gnomad4 OTH exome AF: 0.662

GnomAD4 genome AF: 0.658 AC: 99966 AN: 151922 Hom.: 33412 Cov.: 32 AF XY: 0.651 AC XY: 48325 AN XY: 74268

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.629

Alfa AF: 0.683 Hom.: 83023

Bravo AF: 0.640

Asia WGS AF: 0.552 AC: 1920 AN: 3478

EpiCase AF: 0.693

EpiControl AF: 0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.0
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509701; hg19: chr19-53384185; COSMIC: COSV67088179; COSMIC: COSV67088179;