NM_001351774.2:c.1194G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351774.2. 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
	ZNF320	NM_001351774.2	MANE Select	c.1194G>A	p.Ala398Ala	synonymous	Exon 6 of 6	NP_001338703.1	A2RRD8
	ZNF320	NM_001351773.2		c.1194G>A	p.Ala398Ala	synonymous	Exon 4 of 4	NP_001338702.1	A2RRD8
	ZNF320	NM_001351775.2		c.1194G>A	p.Ala398Ala	synonymous	Exon 6 of 6	NP_001338704.1	A2RRD8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF320	ENST00000682928.1	MANE Select	c.1194G>A	p.Ala398Ala	synonymous	Exon 6 of 6	ENSP00000506814.1	A2RRD8
	ZNF320	ENST00000391781.6	TSL:1	c.1194G>A	p.Ala398Ala	synonymous	Exon 3 of 3	ENSP00000375660.2	A2RRD8
	ZNF320	ENST00000595635.5	TSL:2	c.1194G>A	p.Ala398Ala	synonymous	Exon 8 of 8	ENSP00000473091.1	A2RRD8

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

GnomAD2 exomes AF: 0.620 AC: 155639 AN: 251208 AF XY: 0.631

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 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

African (AFR) AF: 0.679 AC: 22729 AN: 33480

American (AMR) AF: 0.408 AC: 18261 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 17720 AN: 26132

East Asian (EAS) AF: 0.410 AC: 16260 AN: 39694

South Asian (SAS) AF: 0.634 AC: 54643 AN: 86248

European-Finnish (FIN) AF: 0.707 AC: 37771 AN: 53414

Middle Eastern (MID) AF: 0.652 AC: 3759 AN: 5766

European-Non Finnish (NFE) AF: 0.703 AC: 781577 AN: 1111926

Other (OTH) AF: 0.662 AC: 39960 AN: 60390

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

African (AFR) AF: 0.675 AC: 27992 AN: 41460

American (AMR) AF: 0.512 AC: 7807 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2379 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1973 AN: 5130

South Asian (SAS) AF: 0.630 AC: 3033 AN: 4816

European-Finnish (FIN) AF: 0.710 AC: 7477 AN: 10528

Middle Eastern (MID) AF: 0.594 AC: 171 AN: 288

European-Non Finnish (NFE) AF: 0.694 AC: 47138 AN: 67966

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.678 Hom.: 157850

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.0
DANN	Benign	0.50
PhyloP100		-3.6
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: rs6509701; hg19: chr19-53384185; COSMIC: COSV67088179; COSMIC: COSV67088179;