rs6789283

Variant names:

• chr3-21980455-T-C
• rs6789283
• ENST00000494118.5:n.326-130736A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-21980455-T-C
• chr3-21980455-T-G

Variant summary

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

The ENST00000706131.1(ZNF385D):​c.325+188362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,114 control chromosomes in the GnomAD database, including 5,781 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 0.17 (5781 hom., cov: 32)
• Consequence: ZNF385D ENST00000706131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706131.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.326-130736A>G		intron	N/A	ENSP00000493727.1	A0A2R8Y4E5
	ZNF385D	ENST00000706131.1		c.325+188362A>G		intron	N/A	ENSP00000516216.1	A0A994J5P6
	ZNF385D	ENST00000494108.3	TSL:5	c.325+188362A>G		intron	N/A	ENSP00000495609.3	A0A2R8YG37

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26131 AN: 151996 Hom.: 5755 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.172 AC: 26204 AN: 152114 Hom.: 5781 Cov.: 32 AF XY: 0.168 AC XY: 12498 AN XY: 74368

African (AFR) AF: 0.518 AC: 21478 AN: 41438

American (AMR) AF: 0.0819 AC: 1250 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0649 AC: 313 AN: 4826

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2241 AN: 68018

Other (OTH) AF: 0.131 AC: 277 AN: 2116

Alfa AF: 0.0914 Hom.: 1006

Bravo AF: 0.192

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.72
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6789283;

hg19: chr3-22021947;