chrX-85244123-AGGCGGC-A

Variant names:

• chrX-85244123-AGGCGGC-A
• rs758475553
• NM_001330574.2:c.-455_-450delGGCGGC

Variant summary

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

The NM_001330574.2(ZNF711):​c.-455_-450delGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000163 in 147,304 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., 5 hem., cov: 20)
  • Exomes 𝑓: 0.00010 (0 hom. 1 hem.)
• Consequence: ZNF711 NM_001330574.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933
• 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 5 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2	c.-455_-450delGGCGGC		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.-455_-450delGGCGGC		5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1
ZNF711	ENST00000276123.7	c.-450_-445delGGCGGC		5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3
ZNF711	ENST00000373165.7	c.-196_-191delGGCGGC		5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3
SATL1	ENST00000646235.1	c.-1437_-1432delGCCGCC		upstream_gene_variant				ENSP00000495329.1

Frequencies

GnomAD3 genomes AF: 0.000185 AC: 20 AN: 108388 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000409

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000962

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000115

Gnomad OTH AF: 0.000689

GnomAD4 exome AF: 0.000103 AC: 4 AN: 38887 Hom.: 0 AF XY: 0.0000587 AC XY: 1 AN XY: 17049

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

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

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 658

East Asian (EAS) AF: 0.00 AC: 0 AN: 2220

South Asian (SAS) AF: 0.000545 AC: 1 AN: 1834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2554

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

European-Non Finnish (NFE) AF: 0.000108 AC: 3 AN: 27692

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

GnomAD4 genome AF: 0.000184 AC: 20 AN: 108417 Hom.: 0 Cov.: 20 AF XY: 0.000159 AC XY: 5 AN XY: 31515

African (AFR) AF: 0.000408 AC: 12 AN: 29401

American (AMR) AF: 0.0000961 AC: 1 AN: 10407

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2613

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: 0.000115 AC: 6 AN: 52060

Other (OTH) AF: 0.000680 AC: 1 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		0.93
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;