rs1026686

Variant names:

• chr3-21464570-T-C
• rs1026686
• NM_024697.3:c.440-27367A>G

Variant summary

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

The NM_024697.3(ZNF385D):​c.440-27367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,006 control chromosomes in the GnomAD database, including 4,575 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 0.24 (4575 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 0 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024697.3. 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
	ZNF385D	NM_024697.3	MANE Select	c.440-27367A>G		intron	N/A	NP_078973.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000281523.8	TSL:1 MANE Select	c.440-27367A>G		intron	N/A	ENSP00000281523.2
	ZNF385D	ENST00000494118.5	TSL:1	n.*250-5121A>G		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.743-22828A>G		intron	N/A	ENSP00000516216.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36252 AN: 151888 Hom.: 4572 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36296 AN: 152006 Hom.: 4575 Cov.: 31 AF XY: 0.239 AC XY: 17745 AN XY: 74286

African (AFR) AF: 0.296 AC: 12280 AN: 41424

American (AMR) AF: 0.238 AC: 3638 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.110 AC: 568 AN: 5158

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4812

European-Finnish (FIN) AF: 0.237 AC: 2502 AN: 10566

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14108 AN: 67976

Other (OTH) AF: 0.262 AC: 555 AN: 2116

Alfa AF: 0.232 Hom.: 567

Bravo AF: 0.243

Asia WGS AF: 0.195 AC: 677 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1026686; hg19: chr3-21506062;