3-22129805-A-T

Variant names:

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

Variant summary

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

The ENST00000706131.1(ZNF385D):​c.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 ENST00000706131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.325+39012T>A		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.325+39012T>A		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_047448956.1	c.9+39012T>A		intron_variant	Intron 1 of 9		XP_047304912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.325+39012T>A		intron_variant	Intron 2 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.325+39012T>A		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.325+39012T>A		intron_variant	Intron 3 of 9	5		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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.539

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6797769; hg19: chr3-22171297;