Variant 3-21664877-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF385D	NM_024697.3 linkuse as main transcript	c.165+9C>T		intron_variant		ENST00000281523.8	NP_078973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8 linkuse as main transcript	c.165+9C>T		intron_variant		1	NM_024697.3	ENSP00000281523

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

GnomAD3 exomes

AF:

0.119

AC:

29902

AN:

250658

Hom.:

2138

AF XY:

0.114

AC XY:

15503

AN XY:

135448

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 SAS exome

AF:

0.0576

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

Gnomad4 AFR exome

AF:

0.0225

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.0653

Gnomad4 EAS exome

AF:

0.189

Gnomad4 SAS exome

AF:

0.0605

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.116

Gnomad4 OTH exome

AF:

0.0987

GnomAD4 genome

AF:

0.0971

AC:

14773

AN:

152172

Hom.:

973

Cov.:

AF XY:

0.102

AC XY:

7569

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0258

Gnomad4 AMR

AF:

0.127

Gnomad4 ASJ

AF:

0.0548

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.0613

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.0956

Alfa

AF:

0.110

Hom.:

2316

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

DANN

Benign

0.58

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