chr3-22335403-T-C

Variant names:

• chr3-22335403-T-C
• rs9880567
• ENST00000494118.5:n.106+37047A>G

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.106+37047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,070 control chromosomes in the GnomAD database, including 6,595 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 0.29 (6595 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.106+37047A>G		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.106+37047A>G		intron	N/A	ENSP00000516216.1
	ZNF385D	ENST00000494108.3	TSL:5	c.106+37047A>G		intron	N/A	ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43799 AN: 151952 Hom.: 6549 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.289 AC: 43910 AN: 152070 Hom.: 6595 Cov.: 32 AF XY: 0.281 AC XY: 20889 AN XY: 74370

African (AFR) AF: 0.341 AC: 14139 AN: 41482

American (AMR) AF: 0.206 AC: 3150 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3466

East Asian (EAS) AF: 0.153 AC: 791 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4814

European-Finnish (FIN) AF: 0.186 AC: 1974 AN: 10608

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20429 AN: 67922

Other (OTH) AF: 0.293 AC: 619 AN: 2110

Alfa AF: 0.295 Hom.: 10732

Bravo AF: 0.290

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.51
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9880567; hg19: chr3-22376894;