3-21913706-C-T

Variant names:

• chr3-21913706-C-T
• rs11719664
• ENST00000494118.5:n.326-63987G>A

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.326-63987G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,106 control chromosomes in the GnomAD database, including 632 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 0.075 (632 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 10 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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.326-63987G>A		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.326-248678G>A		intron	N/A	ENSP00000516216.1
	ZNF385D	ENST00000494108.3	TSL:5	c.326-248678G>A		intron	N/A	ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11351 AN: 151990 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0747 AC: 11369 AN: 152106 Hom.: 632 Cov.: 32 AF XY: 0.0795 AC XY: 5914 AN XY: 74358

African (AFR) AF: 0.0162 AC: 671 AN: 41542

American (AMR) AF: 0.0504 AC: 769 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.188 AC: 969 AN: 5164

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1385 AN: 10586

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0883 AC: 6001 AN: 67944

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0689 Hom.: 670

Bravo AF: 0.0625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs11719664; hg19: chr3-21955198;