Variant 3-21564619-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_024697.3(ZNF385D):c.231G>A(p.Lys77=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,568,812 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0048 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 42 hom. )

Consequence

ZNF385D
NM_024697.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.61

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:

ZNF385D-AS1 (HGNC:41136): (ZNF385D antisense RNA 1)

ZNF385D-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 3-21564619-C-T is Benign according to our data. Variant chr3-21564619-C-T is described in ClinVar as [Benign]. Clinvar id is 713567.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.61 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF385D	NM_024697.3 linkuse as main transcript	c.231G>A	p.Lys77=	synonymous_variant	3/8	ENST00000281523.8	NP_078973.1
ZNF385D-AS1	NR_046731.1 linkuse as main transcript	n.208-14570C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8 linkuse as main transcript	c.231G>A	p.Lys77=	synonymous_variant	3/8	1	NM_024697.3	ENSP00000281523
ZNF385D-AS1	ENST00000412369.1 linkuse as main transcript	n.181-14570C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00478

AC:

725

AN:

151626

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00136

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00388

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00271

Gnomad FIN

AF:

0.00353

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00732

Gnomad OTH

AF:

0.00720

GnomAD3 exomes

AF:

0.00500

AC:

1141

AN:

228310

Hom.:

AF XY:

0.00498

AC XY:

619

AN XY:

124348

show subpopulations

Gnomad AFR exome

AF:

0.00119

Gnomad AMR exome

AF:

0.00263

Gnomad ASJ exome

AF:

0.00823

Gnomad EAS exome

AF:

0.0000632

Gnomad SAS exome

AF:

0.00207

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.00784

Gnomad OTH exome

AF:

0.00508

GnomAD4 exome

AF:

0.00599

AC:

8488

AN:

1417068

Hom.:

Cov.:

AF XY:

0.00595

AC XY:

4191

AN XY:

704956

show subpopulations

Gnomad4 AFR exome

AF:

0.000855

Gnomad4 AMR exome

AF:

0.00321

Gnomad4 ASJ exome

AF:

0.00830

Gnomad4 EAS exome

AF:

0.0000269

Gnomad4 SAS exome

AF:

0.00223

Gnomad4 FIN exome

AF:

0.00237

Gnomad4 NFE exome

AF:

0.00689

Gnomad4 OTH exome

AF:

0.00520

GnomAD4 genome

AF:

0.00478

AC:

725

AN:

151744

Hom.:

Cov.:

AF XY:

0.00410

AC XY:

304

AN XY:

74134

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00387

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00271

Gnomad4 FIN

AF:

0.00353

Gnomad4 NFE

AF:

0.00732

Gnomad4 OTH

AF:

0.00712

Alfa

AF:

0.00641

Hom.:

Bravo

AF:

0.00488

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.86

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over