Genetic Variant ZNF674:c.*1120_*1121delTA (chrX-46498721-CTA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001190417.2(ZNF674):c.*1120_*1121delTA 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

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 0.491

Variant links:

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]

ZNF674 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ZNF674	NM_001190417.2 link	c.1120_1121delTA	3_prime_UTR_variant	Exon 6 of 6	ENST00000683375.1	NP_001177346.1	Q2M3X9A0A804HHU7
ZNF674	NM_001039891.3 link	c.1120_1121delTA	3_prime_UTR_variant	Exon 6 of 6		NP_001034980.1	Q2M3X9-1
ZNF674	NM_001146291.2 link	c.1120_1121delTA	3_prime_UTR_variant	Exon 6 of 6		NP_001139763.1	Q2M3X9-2
ZNF674	XM_011543943.4 link	c.1120_1121delTA	3_prime_UTR_variant	Exon 6 of 6		XP_011542245.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF674	ENST00000683375.1 link	c.1120_1121delTA		3_prime_UTR_variant	Exon 6 of 6		NM_001190417.2	ENSP00000506769.1		A0A804HHU7
ZNF674	ENST00000523374.5 link	c.1120_1121delTA		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000429148.1		Q2M3X9-1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

20430

AN:

82231

Hom.:

2234

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.248

AC:

20426

AN:

82225

Hom.:

2234

Cov.:

AF XY:

0.164

AC XY:

2637

AN XY:

16069

show subpopulations

African (AFR)

AF:

0.173

AC:

3799

AN:

21976

American (AMR)

AF:

0.244

AC:

1722

AN:

7061

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

627

AN:

2215

East Asian (EAS)

AF:

0.107

AC:

258

AN:

2411

South Asian (SAS)

AF:

0.195

AC:

302

AN:

1547

European-Finnish (FIN)

AF:

0.172

AC:

405

AN:

2356

Middle Eastern (MID)

AF:

0.360

AC:

AN:

136

European-Non Finnish (NFE)

AF:

0.300

AC:

12882

AN:

42934

Other (OTH)

AF:

0.252

AC:

265

AN:

1050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

536

1072

1609

2145

2681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.206

Hom.:

884

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Non-syndromic X-linked intellectual disability

Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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X-46498721-CTA-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over