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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.326-248678G>A		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.326-248678G>A		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_047448956.1	c.10-63987G>A		intron_variant	Intron 1 of 9		XP_047304912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.326-63987G>A		intron_variant	Intron 2 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.326-248678G>A		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.326-248678G>A		intron_variant	Intron 3 of 9	5		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 v4.3

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;