rs1679255

Variant names:

• chr3-22006442-C-T
• rs1679255
• ENST00000494118.5:n.326-156723G>A

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.326-156723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,954 control chromosomes in the GnomAD database, including 45,529 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 0.77 (45529 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.325+162375G>A		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.325+162375G>A		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_047448956.1	c.10-156723G>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.326-156723G>A		intron_variant	Intron 2 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.325+162375G>A		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.325+162375G>A		intron_variant	Intron 3 of 9	5		ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116672 AN: 151838 Hom.: 45498 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.768 AC: 116751 AN: 151954 Hom.: 45529 Cov.: 32 AF XY: 0.768 AC XY: 57059 AN XY: 74276

African (AFR) AF: 0.784 AC: 32549 AN: 41504

American (AMR) AF: 0.582 AC: 8888 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2656 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2554 AN: 5144

South Asian (SAS) AF: 0.813 AC: 3922 AN: 4822

European-Finnish (FIN) AF: 0.879 AC: 9298 AN: 10576

Middle Eastern (MID) AF: 0.741 AC: 215 AN: 290

European-Non Finnish (NFE) AF: 0.801 AC: 54342 AN: 67860

Other (OTH) AF: 0.753 AC: 1588 AN: 2108

Alfa AF: 0.788 Hom.: 23110

Bravo AF: 0.743

Asia WGS AF: 0.653 AC: 2263 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.19
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs1679255; hg19: chr3-22047934;