dbSNP rs3821396: ZNF385D:c.165+9C>T (chr3-21664877-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_024697.3(ZNF385D):c.165+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,613,202 control chromosomes in the GnomAD database, including 11,660 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 0.097 ( 973 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10687 hom. )

Consequence

ZNF385D
NM_024697.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.473

Publications

18 publications found

Variant links:

Genes affected

ZNF385D (HGNC:26191): (zinc finger protein 385D) Enables sequence-specific double-stranded DNA binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF385D 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3 link	c.165+9C>T		intron_variant	Intron 2 of 7	ENST00000281523.8	NP_078973.1	Q9H6B1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8 link	c.165+9C>T		intron_variant	Intron 2 of 7	1	NM_024697.3	ENSP00000281523.2		Q9H6B1

Frequencies

GnomAD3 genomes

AF:

0.0971

AC:

14771

AN:

152054

Hom.:

975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0259

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.0548

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.0621

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0919

GnomAD2 exomes

AF:

0.119

AC:

29902

AN:

250658

AF XY:

0.114

show subpopulations

Gnomad AFR exome

AF:

0.0247

Gnomad AMR exome

AF:

0.164

Gnomad ASJ exome

AF:

0.0648

Gnomad EAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.115

AC:

168098

AN:

1461030

Hom.:

10687

Cov.:

AF XY:

0.113

AC XY:

82371

AN XY:

726840

show subpopulations

African (AFR)

AF:

0.0225

AC:

752

AN:

33430

American (AMR)

AF:

0.161

AC:

7182

AN:

44682

Ashkenazi Jewish (ASJ)

AF:

0.0653

AC:

1705

AN:

26110

East Asian (EAS)

AF:

0.189

AC:

7483

AN:

39670

South Asian (SAS)

AF:

0.0605

AC:

5218

AN:

86218

European-Finnish (FIN)

AF:

0.203

AC:

10810

AN:

53346

Middle Eastern (MID)

AF:

0.0575

AC:

331

AN:

5758

European-Non Finnish (NFE)

AF:

0.116

AC:

128662

AN:

1111470

Other (OTH)

AF:

0.0987

AC:

5955

AN:

60346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

7492

14984

22475

29967

37459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4620

9240

13860

18480

23100

<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:

0.0971

AC:

14773

AN:

152172

Hom.:

973

Cov.:

AF XY:

0.102

AC XY:

7569

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0258

AC:

1073

AN:

41554

American (AMR)

AF:

0.127

AC:

1935

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0548

AC:

190

AN:

3470

East Asian (EAS)

AF:

0.156

AC:

803

AN:

5160

South Asian (SAS)

AF:

0.0613

AC:

296

AN:

4828

European-Finnish (FIN)

AF:

0.218

AC:

2312

AN:

10586

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7831

AN:

67988

Other (OTH)

AF:

0.0956

AC:

202

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

657

1314

1972

2629

3286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.108

Hom.:

3676

Bravo

AF:

0.0904

Asia WGS

AF:

0.106

AC:

367

AN:

3478

EpiCase

AF:

0.106

EpiControl

AF:

0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.3

(source)

DANN

Benign

0.58

PhyloP100

0.47

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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