rs1457590

Positions:

• chr3-21514482-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024697.3(ZNF385D):​c.277-3459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,842 control chromosomes in the GnomAD database, including 30,771 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 0.64 (30771 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	NM_024697.3	c.277-3459G>A		intron_variant		ENST00000281523.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000281523.8	c.277-3459G>A		intron_variant		1	NM_024697.3

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96398 AN: 151724 Hom.: 30736 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.585

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.635 AC: 96479 AN: 151842 Hom.: 30771 Cov.: 31 AF XY: 0.636 AC XY: 47202 AN XY: 74184

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.581

Alfa AF: 0.601 Hom.: 19486

Bravo AF: 0.635

Asia WGS AF: 0.624 AC: 2171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.79

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

Other links and lift over

dbSNP: rs1457590; hg19: chr3-21555974;