7-55901572-G-A

Variant names:

• chr7-55901572-G-A
• rs7790255
• NM_182633.3:c.-582-4681G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182633.3(ZNF713):​c.-582-4681G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,200 control chromosomes in the GnomAD database, including 51,857 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 0.82 (51857 hom., cov: 32)
• Consequence: ZNF713 NM_182633.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 6 publications found

Genes affected

ZNF713 (HGNC:22043): (zinc finger protein 713) The protein encoded by this gene contains C2H2 zinc finger domains. In some individuals, a CGG-repeat expansion from 5-22 repeats to 68-450 repeats has been identified in the first intron of this gene. This mutation is thought to effect the expression of this gene and it has been proposed that it may be associated with Autistic Spectrum Disorder. [provided by RefSeq, Jul 2016]

ZNF713 Gene-Disease associations (from GenCC):

• autism

  Inheritance: AD Classification: LIMITED Submitted by: G2P

ENSG00000249773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182633.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF713	NM_182633.3	MANE Select	c.-582-4681G>A		intron	N/A	NP_872439.2
	ZNF713	NM_001366796.2		c.-589-4681G>A		intron	N/A	NP_001353725.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF713	ENST00000429591.4	TSL:5 MANE Select	c.-582-4681G>A		intron	N/A	ENSP00000416662.3
	ENSG00000249773	ENST00000426595.1	TSL:5	c.-589-4681G>A		intron	N/A	ENSP00000390331.1
	ZNF713	ENST00000411863.2	TSL:5	n.-582-4681G>A		intron	N/A	ENSP00000416974.2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124869 AN: 152082 Hom.: 51801 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.790

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.821 AC: 124982 AN: 152200 Hom.: 51857 Cov.: 32 AF XY: 0.821 AC XY: 61069 AN XY: 74420

African (AFR) AF: 0.950 AC: 39497 AN: 41560

American (AMR) AF: 0.765 AC: 11696 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2686 AN: 3470

East Asian (EAS) AF: 0.952 AC: 4935 AN: 5184

South Asian (SAS) AF: 0.772 AC: 3725 AN: 4824

European-Finnish (FIN) AF: 0.786 AC: 8317 AN: 10578

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51529 AN: 67986

Other (OTH) AF: 0.788 AC: 1662 AN: 2108

Alfa AF: 0.752 Hom.: 4447

Bravo AF: 0.827

Asia WGS AF: 0.833 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-0.86

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: rs7790255; hg19: chr7-55969265;