3-21678377-G-C

Variant summary

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

The NM_024697.3(ZNF385D):c.23-13349C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,074 control chromosomes in the GnomAD database, including 366 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 0.064 (366 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	NM_024697.3	c.23-13349C>G		intron_variant		ENST00000281523.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000281523.8	c.23-13349C>G		intron_variant		1	NM_024697.3

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9767 AN: 151956 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0315

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0643 AC: 9783 AN: 152074 Hom.: 366 Cov.: 32 AF XY: 0.0624 AC XY: 4636 AN XY: 74334

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0315

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.0661

Gnomad4 OTH AF: 0.0689

Alfa AF: 0.0281 Hom.: 18

Bravo AF: 0.0648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.80
Dann	Benign	0.41

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: rs9310651; hg19: chr3-21719869;