NM_001330574.2:c.-452_-450delGGC

Variant names:

• chrX-85244123-AGGC-A
• rs758475553
• NM_001330574.2:c.-452_-450delGGC

Variant summary

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

The NM_001330574.2(ZNF711):​c.-452_-450delGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000712 in 146,046 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., 3 hem., cov: 20)
  • Exomes 𝑓: 0.0021 (0 hom. 1 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 3 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2	c.-452_-450delGGC		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.-452_-450delGGC		5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1
ZNF711	ENST00000276123	c.-447_-445delGGC		5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3
ZNF711	ENST00000373165	c.-193_-191delGGC		5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3
SATL1	ENST00000646235.1	c.-1434_-1432delGCC		upstream_gene_variant				ENSP00000495329.1

Frequencies

GnomAD3 genomes AF: 0.000221 AC: 24 AN: 108378 Hom.: 0 Cov.: 20 AF XY: 0.0000953 AC XY: 3 AN XY: 31470

Gnomad AFR AF: 0.000613

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000294

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00429

Gnomad NFE AF: 0.0000768

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00213 AC: 80 AN: 37640 Hom.: 0 AF XY: 0.0000615 AC XY: 1 AN XY: 16270

Gnomad4 AFR exome AF: 0.00150

Gnomad4 AMR exome AF: 0.00445

Gnomad4 ASJ exome AF: 0.00156

Gnomad4 EAS exome AF: 0.00139

Gnomad4 SAS exome AF: 0.00226

Gnomad4 FIN exome AF: 0.00362

Gnomad4 NFE exome AF: 0.00194

Gnomad4 OTH exome AF: 0.00285

GnomAD4 genome AF: 0.000221 AC: 24 AN: 108406 Hom.: 0 Cov.: 20 AF XY: 0.0000952 AC XY: 3 AN XY: 31508

Gnomad4 AFR AF: 0.000612

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000295

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000768

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs758475553; hg19: chrX-84499129;