rs4538394

Variant names:

• chr3-21758217-A-C
• rs4538394
• ENST00000494118.5:n.389+91439T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-21758217-A-C
• chr3-21758217-A-G
• chr3-21758217-A-T

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.389+91439T>G variant causes a intron 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: 32)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• 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: 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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.326-93189T>G		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.326-93189T>G		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_017007193.2	c.112+91439T>G		intron_variant	Intron 2 of 9		XP_016862682.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.389+91439T>G		intron_variant	Intron 3 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.326-93189T>G		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.326-93189T>G		intron_variant	Intron 3 of 9	5		ENSP00000495609.3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.45
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4538394; hg19: chr3-21799709;