NM_024697.3:c.165+36159C>T

Variant names:

• chr3-21628727-G-A
• rs3911499
• NM_024697.3:c.165+36159C>T

Variant summary

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

The NM_024697.3(ZNF385D):​c.165+36159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,790 control chromosomes in the GnomAD database, including 23,073 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 0.54 (23073 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.802
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024697.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	NM_024697.3	MANE Select	c.165+36159C>T		intron	N/A	NP_078973.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF385D	ENST00000281523.8	TSL:1 MANE Select	c.165+36159C>T		intron	N/A	ENSP00000281523.2
	ZNF385D	ENST00000494118.5	TSL:1	n.390-64043C>T		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.468+36159C>T		intron	N/A	ENSP00000516216.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82400 AN: 151672 Hom.: 23035 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.543 AC: 82492 AN: 151790 Hom.: 23073 Cov.: 31 AF XY: 0.549 AC XY: 40720 AN XY: 74156

African (AFR) AF: 0.428 AC: 17708 AN: 41370

American (AMR) AF: 0.620 AC: 9431 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3114 AN: 5128

South Asian (SAS) AF: 0.620 AC: 2980 AN: 4804

European-Finnish (FIN) AF: 0.682 AC: 7181 AN: 10532

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38412 AN: 67948

Other (OTH) AF: 0.540 AC: 1142 AN: 2114

Alfa AF: 0.556 Hom.: 14036

Bravo AF: 0.530

Asia WGS AF: 0.591 AC: 2056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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: rs3911499; hg19: chr3-21670219;