Genetic Variant NM_001190417.2: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

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

intellectual disability
Inheritance: XL Classification: NO_KNOWN Submitted by: Ambry Genetics
X-linked intellectual disability
Inheritance: XL Classification: NO_KNOWN Submitted by: ClinGen

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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NM_001190417.2:c.1120_1121delTA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over