X-46498721-CTA-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001190417.2(ZNF674):c.*1120_*1121del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.25 (2234 hom., 2637 hem., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: ZNF674 NM_001190417.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.491

Genes affected

ZNF674 (HGNC:17625): (zinc finger protein 674) This gene encodes a zinc finger protein with an N-terminal Kruppel-associated box-containing (KRAB) domain and 11 Kruppel-type C2H2 zinc finger domains. Like other zinc finger proteins, this gene may function as a transcription factor. This gene resides on an area of chromosome X that has been implicated in nonsyndromic X-linked cognitive disabilities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF674	NM_001190417.2	c.*1120_*1121del		3_prime_UTR_variant	6/6	ENST00000683375.1
ZNF674	NM_001039891.3	c.*1120_*1121del		3_prime_UTR_variant	6/6
ZNF674	NM_001146291.2	c.*1120_*1121del		3_prime_UTR_variant	6/6
ZNF674	XM_011543943.4	c.*1120_*1121del		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF674	ENST00000683375.1	c.*1120_*1121del		3_prime_UTR_variant	6/6		NM_001190417.2	A1
ZNF674	ENST00000523374.5	c.*1120_*1121del		3_prime_UTR_variant	6/6	1		P4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 20430 AN: 82231 Hom.: 2234 Cov.: 0 AF XY: 0.164 AC XY: 2635 AN XY: 16069 FAILED QC

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.257

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 9 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 9

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.248 AC: 20426 AN: 82225 Hom.: 2234 Cov.: 0 AF XY: 0.164 AC XY: 2637 AN XY: 16069

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.252

Alfa AF: 0.206 Hom.: 884

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Non-syndromic X-linked intellectual disability Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs1491247337; hg19: chrX-46358156;