3-21924618-T-C

Variant names:

• chr3-21924618-T-C
• rs1694037
• ENST00000494118.5:n.326-74899A>G

Variant summary

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

The ENST00000706131.1(ZNF385D):​c.325+244199A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,218 control chromosomes in the GnomAD database, including 63,992 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 0.92 (63992 hom., cov: 32)
• Consequence: ZNF385D ENST00000706131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.326-74899A>G		intron	N/A	ENSP00000493727.1	A0A2R8Y4E5
	ZNF385D	ENST00000706131.1		c.325+244199A>G		intron	N/A	ENSP00000516216.1	A0A994J5P6
	ZNF385D	ENST00000494108.3	TSL:5	c.325+244199A>G		intron	N/A	ENSP00000495609.3	A0A2R8YG37

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139350 AN: 152098 Hom.: 63933 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.916 AC: 139468 AN: 152218 Hom.: 63992 Cov.: 32 AF XY: 0.916 AC XY: 68158 AN XY: 74436

African (AFR) AF: 0.959 AC: 39805 AN: 41526

American (AMR) AF: 0.929 AC: 14203 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3021 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5096 AN: 5174

South Asian (SAS) AF: 0.942 AC: 4546 AN: 4826

European-Finnish (FIN) AF: 0.862 AC: 9156 AN: 10616

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60756 AN: 68000

Other (OTH) AF: 0.912 AC: 1924 AN: 2110

Alfa AF: 0.903 Hom.: 31116

Bravo AF: 0.923

Asia WGS AF: 0.968 AC: 3365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.64
PhyloP100		-3.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1694037;

hg19: chr3-21966110;