3-22129805-A-T

Variant names:

• chr3-22129805-A-T
• rs6797769
• ENST00000494118.5:n.325+39012T>A

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.325+39012T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,868 control chromosomes in the GnomAD database, including 20,741 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 0.52 (20741 hom., cov: 31)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000494118.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.325+39012T>A		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.325+39012T>A		intron	N/A	ENSP00000516216.1
	ZNF385D	ENST00000494108.3	TSL:5	c.325+39012T>A		intron	N/A	ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78847 AN: 151750 Hom.: 20729 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.519 AC: 78891 AN: 151868 Hom.: 20741 Cov.: 31 AF XY: 0.517 AC XY: 38349 AN XY: 74206

African (AFR) AF: 0.456 AC: 18871 AN: 41424

American (AMR) AF: 0.532 AC: 8112 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2100 AN: 5112

South Asian (SAS) AF: 0.511 AC: 2458 AN: 4810

European-Finnish (FIN) AF: 0.533 AC: 5631 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.555 AC: 37689 AN: 67934

Other (OTH) AF: 0.539 AC: 1136 AN: 2108

Alfa AF: 0.528 Hom.: 2666

Bravo AF: 0.516

Asia WGS AF: 0.478 AC: 1662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.46
DANN	Benign	0.21
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6797769; hg19: chr3-22171297;