chrX-85244123-A-AGGCGGCGGCGGC

Variant names:

• chrX-85244123-A-AGGCGGCGGCGGC
• rs758475553
• NM_001330574.2:c.-461_-450dupGGCGGCGGCGGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001330574.2(ZNF711):​c.-461_-450dupGGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00026 (0 hom., 5 hem., cov: 20)
  • Exomes 𝑓: 0.00023 (0 hom. 4 hem.)
• Consequence: ZNF711 NM_001330574.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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]

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Hemizygotes in GnomAd4 at 5 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2	c.-461_-450dupGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 11	ENST00000674551.1	NP_001317503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF711	ENST00000674551	c.-461_-450dupGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1
ZNF711	ENST00000276123	c.-456_-445dupGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3
ZNF711	ENST00000373165	c.-202_-191dupGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3
SATL1	ENST00000646235.1	c.-1443_-1432dupGCCGCCGCCGCC		upstream_gene_variant				ENSP00000495329.1

Frequencies

GnomAD3 genomes AF: 0.000258 AC: 28 AN: 108387 Hom.: 0 Cov.: 20 AF XY: 0.000159 AC XY: 5 AN XY: 31475

Gnomad AFR AF: 0.000307

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000962

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000230

Gnomad OTH AF: 0.00138

GnomAD4 exome AF: 0.000231 AC: 9 AN: 38904 Hom.: 0 Cov.: 0 AF XY: 0.000235 AC XY: 4 AN XY: 17056

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000544

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000217

Gnomad4 OTH exome AF: 0.000924

GnomAD4 genome AF: 0.000258 AC: 28 AN: 108416 Hom.: 0 Cov.: 20 AF XY: 0.000159 AC XY: 5 AN XY: 31514

Gnomad4 AFR AF: 0.000306

Gnomad4 AMR AF: 0.0000961

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000231

Gnomad4 OTH AF: 0.00136

ClinVar

Not reported in ClinVar

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;