3-21913706-C-T

Variant summary

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

The ENST00000494118.5(ZNF385D):c.326-63987G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,106 control chromosomes in the GnomAD database, including 632 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 0.075 (632 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	XM_011534122.3	c.326-248678G>A		intron_variant
ZNF385D	XM_011534123.3	c.326-248678G>A		intron_variant
ZNF385D	XM_011534124.4	c.326-248678G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000494118.5	c.326-63987G>A		intron_variant, NMD_transcript_variant		1
ZNF385D	ENST00000494108.3	c.326-248678G>A		intron_variant		5		P2
ZNF385D	ENST00000706131.1	c.326-248678G>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11351 AN: 151990 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0747 AC: 11369 AN: 152106 Hom.: 632 Cov.: 32 AF XY: 0.0795 AC XY: 5914 AN XY: 74358

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0883

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0751 Hom.: 472

Bravo AF: 0.0625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	5.6
Dann	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11719664; hg19: chr3-21955198;