Genetic Variant ZNF664:c.*2065G>A (chr12-124014995-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152437.3(ZNF664):c.*2065G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 166,918 control chromosomes in the GnomAD database, including 1,171 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1044 hom., cov: 33)

Exomes 𝑓: 0.14 ( 127 hom. )

Consequence

ZNF664
NM_152437.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

29 publications found

Variant links:

Genes affected

ZNF664 (HGNC:25406): (zinc finger protein 664) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF664 links:

ZNF664-RFLNA (HGNC:):

ZNF664-RFLNA links:

RFLNA (HGNC:27051): (refilin A) Predicted to enable filamin binding activity. Predicted to be involved in several processes, including actin filament bundle organization; negative regulation of bone mineralization involved in bone maturation; and negative regulation of chondrocyte development. Predicted to be located in cytoplasm. Predicted to be active in actin filament bundle. [provided by Alliance of Genome Resources, Apr 2022]

RFLNA links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152437.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF664	NM_152437.3	MANE Select	c.*2065G>A	3_prime_UTR	Exon 5 of 5	NP_689650.1
ZNF664	NM_001204298.2		c.*2065G>A	3_prime_UTR	Exon 5 of 5	NP_001191227.1
ZNF664-RFLNA	NM_001204299.3		c.-234+40975G>A	intron	N/A	NP_001191228.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF664	ENST00000337815.9	TSL:1 MANE Select	c.*2065G>A	3_prime_UTR	Exon 5 of 5	ENSP00000337320.4
ZNF664	ENST00000392404.7	TSL:1	c.*2065G>A	3_prime_UTR	Exon 5 of 5	ENSP00000376205.3
ZNF664	ENST00000539644.5	TSL:1	c.*2065G>A	3_prime_UTR	Exon 6 of 6	ENSP00000441405.1

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16936

AN:

151956

Hom.:

1044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0331

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0578

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.138

AC:

2047

AN:

14844

Hom.:

127

Cov.:

AF XY:

0.139

AC XY:

976

AN XY:

7038

show subpopulations

African (AFR)

AF:

0.00

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)

AF:

0.138

AC:

2016

AN:

14654

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.221

AC:

AN:

Other (OTH)

AF:

0.133

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

162

243

324

405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.111

AC:

16936

AN:

152074

Hom.:

1044

Cov.:

AF XY:

0.106

AC XY:

7913

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0330

AC:

1372

AN:

41546

American (AMR)

AF:

0.104

AC:

1587

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

525

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5182

South Asian (SAS)

AF:

0.0583

AC:

281

AN:

4822

European-Finnish (FIN)

AF:

0.140

AC:

1484

AN:

10566

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11128

AN:

67890

Other (OTH)

AF:

0.131

AC:

277

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

652

1303

1955

2606

3258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.141

Hom.:

3834

Asia WGS

AF:

0.0330

AC:

116

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

8.8

(source)

DANN

Benign

0.89

PhyloP100

-0.054

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over