dbSNP rs13222366: ZNF713:c.308-6973G>A (chr7-55932009-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182633.3(ZNF713):c.308-6973G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,002 control chromosomes in the GnomAD database, including 15,252 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 0.44 ( 15252 hom., cov: 32)

Consequence

ZNF713
NM_182633.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.532

Publications

12 publications found

Variant links:

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

ZNF713 links:

ENSG00000249773 (HGNC:):

ENSG00000249773 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF713	NM_182633.3 link	c.308-6973G>A		intron_variant	Intron 6 of 6	ENST00000429591.4	NP_872439.2	Q8N859
ZNF713	NM_001366796.2 link	c.269-6973G>A		intron_variant	Intron 6 of 6		NP_001353725.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF713	ENST00000429591.4 link	c.308-6973G>A	intron_variant	Intron 6 of 6	5	NM_182633.3	ENSP00000416662.3	Q8N859
ZNF713	ENST00000633730.1 link	c.269-6973G>A	intron_variant	Intron 3 of 3	1		ENSP00000487818.1	A0A8I5JYA4
ENSG00000249773	ENST00000426595.1 link	c.268+8310G>A	intron_variant	Intron 6 of 7	5		ENSP00000390331.1	I3L0E3
ZNF713	ENST00000411863.2 link	n.*408-6973G>A	intron_variant	Intron 7 of 8	5		ENSP00000416974.2	F8WD84

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67276

AN:

151882

Hom.:

15242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.488

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.359

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.398

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

GnomAD4 genome

AF:

0.443

AC:

67323

AN:

152002

Hom.:

15252

Cov.:

AF XY:

0.445

AC XY:

33048

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.405

AC:

16801

AN:

41476

American (AMR)

AF:

0.372

AC:

5675

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

1245

AN:

3468

East Asian (EAS)

AF:

0.576

AC:

2967

AN:

5148

South Asian (SAS)

AF:

0.328

AC:

1578

AN:

4816

European-Finnish (FIN)

AF:

0.557

AC:

5882

AN:

10560

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.468

AC:

31786

AN:

67972

Other (OTH)

AF:

0.398

AC:

840

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1928

3855

5783

7710

9638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.439

Hom.:

47008

Bravo

AF:

0.424

Asia WGS

AF:

0.420

AC:

1459

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.8

(source)

DANN

Benign

0.83

PhyloP100

0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over