chr7-55901572-G-A

Position:

• chr7-55901572-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF713	NM_182633.3	c.-582-4681G>A		intron_variant		ENST00000429591.4	NP_872439.2
ZNF713	NM_001366796.2	c.-589-4681G>A		intron_variant			NP_001353725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF713	ENST00000429591.4	c.-582-4681G>A		intron_variant		5	NM_182633.3	ENSP00000416662	P2
ZNF713	ENST00000411863.2	c.-582-4681G>A		intron_variant, NMD_transcript_variant		5		ENSP00000416974
ZNF713	ENST00000466630.5	n.206-4681G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.788

Alfa AF: 0.741 Hom.: 4092

Bravo AF: 0.827

Asia WGS AF: 0.833 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs7790255; hg19: chr7-55969265;