dbSNP rs179320: ZNF701:c.*1723A>C (chr19-52585180-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018260.3(ZNF701):c.*1723A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,238 control chromosomes in the GnomAD database, including 37,484 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 0.70 ( 37441 hom., cov: 32)

Exomes 𝑓: 0.76 ( 43 hom. )

Consequence

ZNF701
NM_018260.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26

Publications

3 publications found

Variant links:

Genes affected

ZNF701 (HGNC:25597): (zinc finger protein 701) 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 by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF701 links:

ENSG00000268886 (HGNC:):

ENSG00000268886 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018260.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF701	NM_018260.3	MANE Select	c.*1723A>C	3_prime_UTR	Exon 4 of 4	NP_060730.2
ZNF701	NM_001172655.1		c.*1723A>C	3_prime_UTR	Exon 5 of 5	NP_001166126.1
ZNF701	NM_001433681.1		c.*1723A>C	3_prime_UTR	Exon 5 of 5	NP_001420610.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF701	ENST00000391785.8	TSL:1 MANE Select	c.*1723A>C	3_prime_UTR	Exon 4 of 4	ENSP00000375662.2
ZNF701	ENST00000540331.1	TSL:1	c.*1723A>C	3_prime_UTR	Exon 5 of 5	ENSP00000444339.1
ENSG00000268886	ENST00000599222.1	TSL:3	n.382T>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106194

AN:

151976

Hom.:

37390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.705

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.717

Gnomad FIN

AF:

0.697

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.738

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.757

AC:

109

AN:

144

Hom.:

Cov.:

AF XY:

0.804

AC XY:

AN XY:

112

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.746

AC:

AN:

118

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.699

AC:

106309

AN:

152094

Hom.:

37441

Cov.:

AF XY:

0.695

AC XY:

51715

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.674

AC:

27951

AN:

41490

American (AMR)

AF:

0.639

AC:

9761

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.705

AC:

2446

AN:

3468

East Asian (EAS)

AF:

0.506

AC:

2608

AN:

5156

South Asian (SAS)

AF:

0.717

AC:

3457

AN:

4822

European-Finnish (FIN)

AF:

0.697

AC:

7375

AN:

10580

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.738

AC:

50181

AN:

67984

Other (OTH)

AF:

0.708

AC:

1496

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1652

3304

4955

6607

8259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.688

Hom.:

4580

Bravo

AF:

0.694

Asia WGS

AF:

0.636

AC:

2214

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.74

(source)

DANN

Benign

0.62

PhyloP100

-3.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over