chr3-21751390-A-T

Variant names:

• chr3-21751390-A-T
• rs7634827
• ENST00000494118.5:n.389+98266T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000963857.1(ZNF385D):​c.-474T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF385D ENST00000963857.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 7 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000963857.1. 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
	ZNF385D	NM_024697.3	MANE Select	c.-474T>A		upstream_gene	N/A	NP_078973.1	Q9H6B1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000494118.5	TSL:1	n.389+98266T>A		intron	N/A	ENSP00000493727.1	A0A2R8Y4E5
	ZNF385D	ENST00000963857.1		c.-474T>A		5_prime_UTR	Exon 1 of 9	ENSP00000633916.1
	ZNF385D	ENST00000706131.1		c.326-86362T>A		intron	N/A	ENSP00000516216.1	A0A994J5P6

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 858890 Hom.: 0 Cov.: 48 AF XY: 0.00 AC XY: 0 AN XY: 397906

African (AFR) AF: 0.00 AC: 0 AN: 16388

American (AMR) AF: 0.00 AC: 0 AN: 2362

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5666

East Asian (EAS) AF: 0.00 AC: 0 AN: 4268

South Asian (SAS) AF: 0.00 AC: 0 AN: 19562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1484

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1710

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 778576

Other (OTH) AF: 0.00 AC: 0 AN: 28874

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 59319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		1.2
PromoterAI		0.0050	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7634827; hg19: chr3-21792882;