3-21426209-C-A

Variant names:

• chr3-21426209-C-A
• rs370898
• NM_024697.3:c.674-539G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024697.3(ZNF385D):​c.674-539G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 151,934 control chromosomes in the GnomAD database, including 62,943 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 0.91 (62943 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3	c.674-539G>T		intron_variant	Intron 5 of 7	ENST00000281523.8	NP_078973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8	c.674-539G>T		intron_variant	Intron 5 of 7	1	NM_024697.3	ENSP00000281523.2

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138066 AN: 151814 Hom.: 62912 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.909 AC: 138153 AN: 151934 Hom.: 62943 Cov.: 32 AF XY: 0.908 AC XY: 67404 AN XY: 74224

African (AFR) AF: 0.865 AC: 35806 AN: 41410

American (AMR) AF: 0.943 AC: 14394 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3307 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4919 AN: 5166

South Asian (SAS) AF: 0.916 AC: 4415 AN: 4818

European-Finnish (FIN) AF: 0.889 AC: 9361 AN: 10534

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62870 AN: 67954

Other (OTH) AF: 0.928 AC: 1959 AN: 2110

Alfa AF: 0.920 Hom.: 34737

Bravo AF: 0.914

Asia WGS AF: 0.936 AC: 3255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		0.18
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: rs370898; hg19: chr3-21467701;