dbSNP rs62621812: ZNF800:p.Pro103Ser (chr7-127375029-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_176814.5(ZNF800):c.307C>T(p.Pro103Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 1,567,422 control chromosomes in the GnomAD database, including 400 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.017 ( 47 hom., cov: 32)

Exomes 𝑓: 0.020 ( 353 hom. )

Consequence

ZNF800
NM_176814.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.89

Publications

36 publications found

Variant links:

Genes affected

ZNF800 (HGNC:27267): (zinc finger protein 800) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF800 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 (MetaRNN=0.0023738742).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0174 (2642/152136) while in subpopulation NFE AF = 0.0247 (1680/67984). AF 95% confidence interval is 0.0237. There are 47 homozygotes in GnomAd4. There are 1393 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 2642 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF800	NM_176814.5 link	c.307C>T	p.Pro103Ser	missense_variant	Exon 5 of 6	ENST00000265827.8	NP_789784.2	Q2TB10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF800	ENST00000265827.8 link	c.307C>T	p.Pro103Ser	missense_variant	Exon 5 of 6	1	NM_176814.5	ENSP00000265827.3		Q2TB10

Frequencies

GnomAD3 genomes

AF:

0.0174

AC:

2644

AN:

152018

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00321

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.00656

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.0562

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0247

Gnomad OTH

AF:

0.0134

GnomAD2 exomes

AF:

0.0178

AC:

3892

AN:

218762

AF XY:

0.0176

show subpopulations

Gnomad AFR exome

AF:

0.00325

Gnomad AMR exome

AF:

0.00685

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.0000581

Gnomad FIN exome

AF:

0.0509

Gnomad NFE exome

AF:

0.0241

Gnomad OTH exome

AF:

0.0201

GnomAD4 exome

AF:

0.0205

AC:

28951

AN:

1415286

Hom.:

353

Cov.:

AF XY:

0.0202

AC XY:

14192

AN XY:

701530

show subpopulations

African (AFR)

AF:

0.00306

AC:

AN:

31684

American (AMR)

AF:

0.00712

AC:

268

AN:

37618

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

355

AN:

23602

East Asian (EAS)

AF:

0.0000254

AC:

AN:

39328

South Asian (SAS)

AF:

0.00361

AC:

286

AN:

79246

European-Finnish (FIN)

AF:

0.0457

AC:

2173

AN:

47558

Middle Eastern (MID)

AF:

0.00906

AC:

AN:

5520

European-Non Finnish (NFE)

AF:

0.0227

AC:

24764

AN:

1092398

Other (OTH)

AF:

0.0164

AC:

957

AN:

58332

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

1286

2572

3859

5145

6431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.0174

AC:

2642

AN:

152136

Hom.:

Cov.:

AF XY:

0.0187

AC XY:

1393

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.00320

AC:

133

AN:

41514

American (AMR)

AF:

0.00656

AC:

100

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.00270

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0562

AC:

595

AN:

10588

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0247

AC:

1680

AN:

67984

Other (OTH)

AF:

0.0132

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

119

238

358

477

596

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0211

Hom.:

139

Bravo

AF:

0.0132

TwinsUK

AF:

0.0221

AC:

ALSPAC

AF:

0.0210

AC:

ESP6500AA

AF:

0.00341

AC:

ESP6500EA

AF:

0.0220

AC:

189

ExAC

AF:

0.0178

AC:

2163

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.80

DEOGEN2

Benign

0.0047

T;T;T;T;T;T

Eigen

Benign

-0.21

Eigen_PC

Benign

0.011

FATHMM_MKL

Uncertain

0.88

LIST_S2

Uncertain

0.86

.;.;D;D;D;D

MetaRNN

Benign

0.0024

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

N;N;N;.;.;.

PhyloP100

2.9

PrimateAI

Uncertain

0.58

PROVEAN

Benign

-0.24

N;N;N;.;N;N

REVEL

Benign

0.078

Sift

Benign

0.32

T;T;T;.;T;T

Sift4G

Benign

0.58

T;T;T;T;T;T

Polyphen

0.15

B;B;B;.;.;.

Vest4

0.16

MPC

0.26

ClinPred

0.0062

GERP RS

4.6

Varity_R

0.042

gMVP

0.47

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over