chrX-85244123-AGGCGGCGGC-A

Variant names:

• chrX-85244123-AGGCGGCGGC-A
• rs758475553
• NM_001330574.2:c.-458_-450delGGCGGCGGC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001330574.2(ZNF711):​c.-458_-450delGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000584 in 147,321 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00073 (0 hom., 15 hem., cov: 20)
  • Exomes 𝑓: 0.00018 (0 hom. 5 hem.)
• Consequence: ZNF711 NM_001330574.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Hemizygotes in GnomAd4 at 15 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2	c.-458_-450delGGCGGCGGC		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	ENST00000674551.1	c.-458_-450delGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1
ZNF711	ENST00000276123.7	c.-453_-445delGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3
ZNF711	ENST00000373165.7	c.-199_-191delGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3
SATL1	ENST00000646235.1	c.-1440_-1432delGCCGCCGCC		upstream_gene_variant				ENSP00000495329.1

Frequencies

GnomAD3 genomes AF: 0.000729 AC: 79 AN: 108385 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000204

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00125

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000499

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000180 AC: 7 AN: 38907 Hom.: 0 AF XY: 0.000293 AC XY: 5 AN XY: 17059

African (AFR) AF: 0.00 AC: 0 AN: 686

American (AMR) AF: 0.00 AC: 0 AN: 917

Ashkenazi Jewish (ASJ) AF: 0.00303 AC: 2 AN: 659

East Asian (EAS) AF: 0.00 AC: 0 AN: 2221

South Asian (SAS) AF: 0.00 AC: 0 AN: 1837

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 160

European-Non Finnish (NFE) AF: 0.000180 AC: 5 AN: 27705

Other (OTH) AF: 0.00 AC: 0 AN: 2166

GnomAD4 genome AF: 0.000729 AC: 79 AN: 108414 Hom.: 0 Cov.: 20 AF XY: 0.000476 AC XY: 15 AN XY: 31512

African (AFR) AF: 0.000204 AC: 6 AN: 29401

American (AMR) AF: 0.00125 AC: 13 AN: 10407

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 34 AN: 2611

East Asian (EAS) AF: 0.00 AC: 0 AN: 3385

South Asian (SAS) AF: 0.00 AC: 0 AN: 2534

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5660

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 213

European-Non Finnish (NFE) AF: 0.000499 AC: 26 AN: 52059

Other (OTH) AF: 0.00 AC: 0 AN: 1471

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8
Mutation Taster		=300/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs758475553; hg19: chrX-84499129;