rs6509701

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-52880932-C-A
• chr19-52880932-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001351774.2(ZNF320):​c.1194G>T​(p.Ala398Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP7: Synonymous conserved (PhyloP=-3.6 with no splicing effect.

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>T	p.Ala398Ala	synonymous	Exon 6 of 6	NP_001338703.1	A2RRD8
	ZNF320	NM_001351773.2		c.1194G>T	p.Ala398Ala	synonymous	Exon 4 of 4	NP_001338702.1	A2RRD8
	ZNF320	NM_001351775.2		c.1194G>T	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>T	p.Ala398Ala	synonymous	Exon 6 of 6	ENSP00000506814.1	A2RRD8
	ZNF320	ENST00000391781.6	TSL:1	c.1194G>T	p.Ala398Ala	synonymous	Exon 3 of 3	ENSP00000375660.2	A2RRD8
	ZNF320	ENST00000595635.5	TSL:2	c.1194G>T	p.Ala398Ala	synonymous	Exon 8 of 8	ENSP00000473091.1	A2RRD8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251208 AF XY: 0.00000737

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 64

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-3.6

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;