chr7-55932009-G-A

Variant names:

• chr7-55932009-G-A
• rs13222366
• NM_182633.3:c.308-6973G>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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 12 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=-0.82).
• 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	c.308-6973G>A		intron_variant	Intron 6 of 6	ENST00000429591.4	NP_872439.2
ZNF713	NM_001366796.2	c.269-6973G>A		intron_variant	Intron 6 of 6		NP_001353725.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67276 AN: 151882 Hom.: 15242 Cov.: 32

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.: 32 AF XY: 0.445 AC XY: 33048 AN XY: 74284

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

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
DANN	Benign	0.83
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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: rs13222366; hg19: chr7-55999702;