chr7-6653711-G-A

Position:

• chr7-6653711-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001278559.2(ZNF316):​c.2115G>A​(p.Ala705=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000983 in 1,097,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00068 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0010 (0 hom.)
• Consequence: ZNF316 NM_001278559.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.419

Genes affected

ZNF316 (HGNC:13843): (zinc finger protein 316) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 7-6653711-G-A is Benign according to our data. Variant chr7-6653711-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657310.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.419 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF316	NM_001278559.2	c.2115G>A	p.Ala705=	synonymous_variant	9/9	ENST00000382252.6
ZNF316	XM_024446618.2	c.2115G>A	p.Ala705=	synonymous_variant	8/8
ZNF316	XM_024446619.2	c.2115G>A	p.Ala705=	synonymous_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF316	ENST00000382252.6	c.2115G>A	p.Ala705=	synonymous_variant	9/9	5	NM_001278559.2	P1

Frequencies

GnomAD3 genomes AF: 0.000680 AC: 100 AN: 147080 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000540

Gnomad ASJ AF: 0.00177

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00114

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00103 AC: 979 AN: 950214 Hom.: 0 Cov.: 34 AF XY: 0.00102 AC XY: 455 AN XY: 446254

Gnomad4 AFR exome AF: 0.000168

Gnomad4 AMR exome AF: 0.000236

Gnomad4 ASJ exome AF: 0.00308

Gnomad4 EAS exome AF: 0.0000658

Gnomad4 SAS exome AF: 0.000545

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00108

Gnomad4 OTH exome AF: 0.000885

GnomAD4 genome AF: 0.000680 AC: 100 AN: 147166 Hom.: 0 Cov.: 33 AF XY: 0.000670 AC XY: 48 AN XY: 71664

Gnomad4 AFR AF: 0.000243

Gnomad4 AMR AF: 0.000539

Gnomad4 ASJ AF: 0.00177

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00114

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000212 Hom.: 0

Bravo AF: 0.000744

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

ZNF316: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.90
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs527903972; hg19: chr7-6693342;