X-85244123-A-AGGC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001330574.2(ZNF711):c.-452_-450dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., 45 hem., cov: 20)
  • Exomes 𝑓: 0.0022 (1 hom. 33 hem.)
• Consequence: ZNF711 NM_001330574.2 5_prime_UTR
• Clinical Significance: Likely 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-85244123-A-AGGC is Benign according to our data. Variant chrX-85244123-A-AGGC is described in ClinVar as [Likely_benign]. Clinvar id is 368738.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd at 46 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF711	NM_001330574.2	c.-452_-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.-452_-450dup		5_prime_UTR_variant	1/11		NM_001330574.2	P1
ZNF711	ENST00000276123.7	c.-447_-445dup		5_prime_UTR_variant	1/10	1
ZNF711	ENST00000373165.7	c.-193_-191dup		5_prime_UTR_variant	1/9	1

Frequencies

GnomAD3 genomes AF: 0.00194 AC: 210 AN: 108386 Hom.: 0 Cov.: 20 AF XY: 0.00146 AC XY: 46 AN XY: 31474

Gnomad AFR AF: 0.00187

Gnomad AMI AF: 0.00149

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00441

Gnomad SAS AF: 0.00747

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00194

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00224 AC: 87 AN: 38889 Hom.: 1 Cov.: 0 AF XY: 0.00194 AC XY: 33 AN XY: 17039

Gnomad4 AFR exome AF: 0.00147

Gnomad4 AMR exome AF: 0.00218

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00225

Gnomad4 SAS exome AF: 0.00327

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00242

Gnomad4 OTH exome AF: 0.00277

GnomAD4 genome AF: 0.00193 AC: 209 AN: 108415 Hom.: 0 Cov.: 20 AF XY: 0.00143 AC XY: 45 AN XY: 31513

Gnomad4 AFR AF: 0.00187

Gnomad4 AMR AF: 0.00183

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00414

Gnomad4 SAS AF: 0.00750

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00194

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Non-syndromic X-linked intellectual disability Benign:1

Likely 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;