3-22080904-C-T

Variant summary

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

The ENST00000494118.5(ZNF385D):c.325+87913G>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 0.266 in 152,002 control chromosomes in the GnomAD database, including 5,431 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 0.27 (5431 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	XM_011534122.3	c.325+87913G>A		intron_variant
ZNF385D	XM_011534123.3	c.325+87913G>A		intron_variant
ZNF385D	XM_011534124.4	c.325+87913G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000494118.5	c.325+87913G>A		intron_variant, NMD_transcript_variant		1
ZNF385D	ENST00000494108.3	c.325+87913G>A		intron_variant		5		P2
ZNF385D	ENST00000706131.1	c.325+87913G>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40399 AN: 151884 Hom.: 5422 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.266 AC: 40431 AN: 152002 Hom.: 5431 Cov.: 32 AF XY: 0.266 AC XY: 19768 AN XY: 74300

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.299

Alfa AF: 0.285 Hom.: 14816

Bravo AF: 0.264

Asia WGS AF: 0.275 AC: 955 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	1.0
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2593321; hg19: chr3-22122396;