rs1026686

chr3-21464570-T-C

Variant summary

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

The NM_024697.3(ZNF385D):c.440-27367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,006 control chromosomes in the GnomAD database, including 4,575 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 0.24 (4575 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	NM_024697.3	c.440-27367A>G		intron_variant		ENST00000281523.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000281523.8	c.440-27367A>G		intron_variant		1	NM_024697.3

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36252 AN: 151888 Hom.: 4572 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36296 AN: 152006 Hom.: 4575 Cov.: 31 AF XY: 0.239 AC XY: 17745 AN XY: 74286

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.262

Alfa AF: 0.229 Hom.: 525

Bravo AF: 0.243

Asia WGS AF: 0.195 AC: 677 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	12
Dann	Benign	0.81

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: rs1026686; hg19: chr3-21506062;