chr3-21660220-A-G

Position:

• chr3-21660220-A-G

Variant summary

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

The NM_024697.3(ZNF385D):​c.165+4666T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 151,976 control chromosomes in the GnomAD database, including 42,514 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 0.75 (42514 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF385D	NM_024697.3	c.165+4666T>C		intron_variant		ENST00000281523.8	NP_078973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8	c.165+4666T>C		intron_variant		1	NM_024697.3	ENSP00000281523

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113126 AN: 151858 Hom.: 42465 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.745 AC: 113230 AN: 151976 Hom.: 42514 Cov.: 32 AF XY: 0.748 AC XY: 55539 AN XY: 74276

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.741

Alfa AF: 0.763 Hom.: 85008

Bravo AF: 0.735

Asia WGS AF: 0.631 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.68

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: rs1320292; hg19: chr3-21701712;