rs9880567

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.106+37047A>G		intron_variant	Intron 1 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.106+37047A>G		intron_variant	Intron 1 of 8		XP_016862681.1
ZNF385D	XM_011534122.3	c.106+37047A>G		intron_variant	Intron 1 of 6		XP_011532424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.106+37047A>G		intron_variant	Intron 1 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.106+37047A>G		intron_variant	Intron 1 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.106+37047A>G		intron_variant	Intron 2 of 9	5		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 v4.3

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;