rs9305035

chr19-9161293-C-Achr19-9161293-C-Gchr19-9161293-C-T

Variant summary

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

The NM_020933.5(ZNF317):c.1648C>A(p.Arg550=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 1,603,104 control chromosomes in the GnomAD database, including 4,812 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 0.098 (864 hom., cov: 32)
  • Exomes 𝑓: 0.070 (3948 hom.)
• Consequence: ZNF317 NM_020933.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

ZNF317 (HGNC:13507): (zinc finger protein 317) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP7: Synonymous conserved (PhyloP=-1.27 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF317	NM_020933.5	c.1648C>A	p.Arg550=	synonymous_variant	7/7	ENST00000247956.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF317	ENST00000247956.11	c.1648C>A	p.Arg550=	synonymous_variant	7/7	1	NM_020933.5	P1

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14812 AN: 150814 Hom.: 854 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0899

GnomAD3 exomes AF: 0.0754 AC: 18804 AN: 249382 Hom.: 790 AF XY: 0.0733 AC XY: 9883 AN XY: 134764

Gnomad AFR exome AF: 0.163

Gnomad AMR exome AF: 0.0761

Gnomad ASJ exome AF: 0.0947

Gnomad EAS exome AF: 0.105

Gnomad SAS exome AF: 0.0585

Gnomad FIN exome AF: 0.0400

Gnomad NFE exome AF: 0.0672

Gnomad OTH exome AF: 0.0765

GnomAD4 exome AF: 0.0699 AC: 101579 AN: 1452168 Hom.: 3948 Cov.: 32 AF XY: 0.0694 AC XY: 50135 AN XY: 722044

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.0819

Gnomad4 ASJ exome AF: 0.0934

Gnomad4 EAS exome AF: 0.0815

Gnomad4 SAS exome AF: 0.0589

Gnomad4 FIN exome AF: 0.0414

Gnomad4 NFE exome AF: 0.0669

Gnomad4 OTH exome AF: 0.0792

GnomAD4 genome AF: 0.0985 AC: 14865 AN: 150936 Hom.: 864 Cov.: 32 AF XY: 0.0980 AC XY: 7231 AN XY: 73780

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0960

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.0952

Gnomad4 SAS AF: 0.0579

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0685 Hom.: 241

Bravo AF: 0.105

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	6.4
Dann	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs9305035; hg19: chr19-9271969; COSMIC: COSV56111060; COSMIC: COSV56111060;