X-85244123-A-AGGCGGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001330574.2(ZNF711):c.-455_-450dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (175 hom., 714 hem., cov: 20)
  • Exomes 𝑓: 0.0026 (5 hom. 34 hem.)
• Consequence: ZNF711 NM_001330574.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.933

Genes affected

ZNF711 (HGNC:13128): (zinc finger protein 711) This gene encodes a zinc finger protein of unknown function. It bears similarity to a zinc finger protein which acts as a transcriptional activator. This gene lies in a region of the X chromosome which has been associated with cognitive disability. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-85244123-A-AGGCGGC is Benign according to our data. Variant chrX-85244123-A-AGGCGGC is described in ClinVar as [Benign]. Clinvar id is 368739.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF711	NM_001330574.2	c.-455_-450dup		5_prime_UTR_variant	1/11	ENST00000674551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF711	ENST00000674551.1	c.-455_-450dup		5_prime_UTR_variant	1/11		NM_001330574.2	P1
ZNF711	ENST00000276123.7	c.-450_-445dup		5_prime_UTR_variant	1/10	1
ZNF711	ENST00000373165.7	c.-196_-191dup		5_prime_UTR_variant	1/9	1

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 3555 AN: 108331 Hom.: 175 Cov.: 20 AF XY: 0.0227 AC XY: 714 AN XY: 31453

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00962

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00429

Gnomad NFE AF: 0.000672

Gnomad OTH AF: 0.0179

GnomAD4 exome AF: 0.00260 AC: 101 AN: 38898 Hom.: 5 Cov.: 0 AF XY: 0.00199 AC XY: 34 AN XY: 17052

Gnomad4 AFR exome AF: 0.0959

Gnomad4 AMR exome AF: 0.00218

Gnomad4 ASJ exome AF: 0.00606

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000544

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000469

Gnomad4 OTH exome AF: 0.00739

GnomAD4 genome AF: 0.0328 AC: 3559 AN: 108360 Hom.: 175 Cov.: 20 AF XY: 0.0227 AC XY: 714 AN XY: 31492

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.00951

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000672

Gnomad4 OTH AF: 0.0177

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Non-syndromic X-linked intellectual disability Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs758475553; hg19: chrX-84499129;