3-21514482-C-T

Variant names:

• chr3-21514482-C-T
• rs1457590
• NM_024697.3:c.277-3459G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3	c.277-3459G>A		intron_variant	Intron 3 of 7	ENST00000281523.8	NP_078973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8	c.277-3459G>A		intron_variant	Intron 3 of 7	1	NM_024697.3	ENSP00000281523.2

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

African (AFR) AF: 0.721 AC: 29869 AN: 41420

American (AMR) AF: 0.569 AC: 8657 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2054 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3497 AN: 5110

South Asian (SAS) AF: 0.657 AC: 3166 AN: 4822

European-Finnish (FIN) AF: 0.652 AC: 6857 AN: 10516

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40312 AN: 67960

Other (OTH) AF: 0.581 AC: 1227 AN: 2112

Alfa AF: 0.601 Hom.: 23015

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
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1457590; hg19: chr3-21555974;