rs1679255

chr3-22006442-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494118.5(ZNF385D):c.326-156723G>A variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZNF385D	XM_011534122.3	c.325+162375G>A		intron_variant
ZNF385D	XM_011534123.3	c.325+162375G>A		intron_variant
ZNF385D	XM_011534124.4	c.325+162375G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000494118.5	c.326-156723G>A		intron_variant, NMD_transcript_variant		1
ZNF385D	ENST00000494108.3	c.325+162375G>A		intron_variant		5		P2
ZNF385D	ENST00000706131.1	c.325+162375G>A		intron_variant				A2

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

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.753

Alfa AF: 0.787 Hom.: 20440

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1679255; hg19: chr3-22047934;