Genetic Variant ZNF385D:n.389+98266T>C (chr3-21751390-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000706131.1(ZNF385D):c.326-86362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 1,010,310 control chromosomes in the GnomAD database, including 246,745 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 0.74 ( 41729 hom., cov: 28)

Exomes 𝑓: 0.69 ( 205016 hom. )

Consequence

ZNF385D
ENST00000706131.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3 link	c.-474T>C		upstream_gene_variant		ENST00000281523.8	NP_078973.1	Q9H6B1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8 link	c.-474T>C		upstream_gene_variant		1	NM_024697.3	ENSP00000281523.2		Q9H6B1

Frequencies

GnomAD3 genomes

AF:

0.737

AC:

111559

AN:

151390

Hom.:

41693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.841

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.744

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.939

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.598

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.682

Gnomad OTH

AF:

0.750

GnomAD4 exome

AF:

0.689

AC:

591874

AN:

858802

Hom.:

205016

Cov.:

AF XY:

0.689

AC XY:

274278

AN XY:

397864

show subpopulations

Gnomad4 AFR exome

AF:

0.843

Gnomad4 AMR exome

AF:

0.704

Gnomad4 ASJ exome

AF:

0.664

Gnomad4 EAS exome

AF:

0.946

Gnomad4 SAS exome

AF:

0.735

Gnomad4 FIN exome

AF:

0.562

Gnomad4 NFE exome

AF:

0.683

Gnomad4 OTH exome

AF:

0.705

GnomAD4 genome

AF:

0.737

AC:

111653

AN:

151508

Hom.:

41729

Cov.:

AF XY:

0.736

AC XY:

54432

AN XY:

73984

show subpopulations

Gnomad4 AFR

AF:

0.841

Gnomad4 AMR

AF:

0.744

Gnomad4 ASJ

AF:

0.678

Gnomad4 EAS

AF:

0.939

Gnomad4 SAS

AF:

0.771

Gnomad4 FIN

AF:

0.598

Gnomad4 NFE

AF:

0.682

Gnomad4 OTH

AF:

0.751

Alfa

AF:

0.688

Hom.:

45043

Bravo

AF:

0.752

Asia WGS

AF:

0.847

AC:

2947

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over