3-21443707-G-C

Variant names:

• chr3-21443707-G-C
• rs6797692
• NM_024697.3:c.440-6504C>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.440-6504C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,042 control chromosomes in the GnomAD database, including 10,341 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 0.33 (10341 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	NM_024697.3	MANE Select	c.440-6504C>G		intron	N/A	NP_078973.1	Q9H6B1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000281523.8	TSL:1 MANE Select	c.440-6504C>G		intron	N/A	ENSP00000281523.2	Q9H6B1
	ZNF385D	ENST00000494118.5	TSL:1	n.*368-6504C>G		intron	N/A	ENSP00000493727.1	A0A2R8Y4E5
	ZNF385D	ENST00000706131.1		c.743-1965C>G		intron	N/A	ENSP00000516216.1	A0A994J5P6

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50462 AN: 151924 Hom.: 10317 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.332 AC: 50536 AN: 152042 Hom.: 10341 Cov.: 32 AF XY: 0.338 AC XY: 25149 AN XY: 74324

African (AFR) AF: 0.573 AC: 23768 AN: 41470

American (AMR) AF: 0.333 AC: 5084 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1873 AN: 5162

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2847 AN: 10554

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13702 AN: 67972

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.259 Hom.: 792

Bravo AF: 0.344

Asia WGS AF: 0.385 AC: 1334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.73
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: rs6797692; hg19: chr3-21485199;