rs6789283

chr3-21980455-T-Cchr3-21980455-T-G

Variant summary

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

The ENST00000494118.5(ZNF385D):c.326-130736A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 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 ENST00000494118.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF385D	XM_011534122.3	c.325+188362A>G		intron_variant
ZNF385D	XM_011534123.3	c.325+188362A>G		intron_variant
ZNF385D	XM_011534124.4	c.325+188362A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF385D	ENST00000494118.5	c.326-130736A>G		intron_variant, NMD_transcript_variant		1
ZNF385D	ENST00000494108.3	c.325+188362A>G		intron_variant		5		P2
ZNF385D	ENST00000706131.1	c.325+188362A>G		intron_variant				A2

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

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0825 Hom.: 575

Bravo AF: 0.192

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.72
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6789283; hg19: chr3-22021947;