rs3860575

Positions:

• chr3-21474213-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.439+36648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,638 control chromosomes in the GnomAD database, including 5,515 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 0.26 (5515 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	NM_024697.3	c.439+36648G>A		intron_variant		ENST00000281523.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000281523.8	c.439+36648G>A		intron_variant		1	NM_024697.3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38975 AN: 151520 Hom.: 5502 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.257 AC: 39036 AN: 151638 Hom.: 5515 Cov.: 31 AF XY: 0.257 AC XY: 19035 AN XY: 74052

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.271

Alfa AF: 0.222 Hom.: 5177

Bravo AF: 0.264

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.38

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: rs3860575; hg19: chr3-21515705;