chr3-22042095-A-G

Position:

• chr3-22042095-A-G

Variant summary

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

The ENST00000706131.1(ZNF385D):​c.325+126722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,964 control chromosomes in the GnomAD database, including 6,385 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 0.28 (6385 hom., cov: 32)
• Consequence: ZNF385D ENST00000706131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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]

ZNF385D (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.325+126722T>C		intron_variant			XP_016862680.1
ZNF385D	XM_017007192.2	c.325+126722T>C		intron_variant			XP_016862681.1
ZNF385D	XM_047448956.1	c.9+126722T>C		intron_variant			XP_047304912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.325+126722T>C		intron_variant		1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.325+126722T>C		intron_variant				ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.325+126722T>C		intron_variant		5		ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43027 AN: 151846 Hom.: 6381 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.283 AC: 43042 AN: 151964 Hom.: 6385 Cov.: 32 AF XY: 0.279 AC XY: 20757 AN XY: 74302

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.293

Alfa AF: 0.323 Hom.: 8206

Bravo AF: 0.289

Asia WGS AF: 0.290 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166315; hg19: chr3-22083587;