3-21678377-G-C

Variant names:

• chr3-21678377-G-C
• rs9310651
• NM_024697.3:c.23-13349C>G

Variant summary

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

The NM_024697.3(ZNF385D):​c.23-13349C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 152,074 control chromosomes in the GnomAD database, including 366 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 0.064 (366 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 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.23-13349C>G		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.23-13349C>G		intron	N/A	ENSP00000281523.2
	ZNF385D	ENST00000494118.5	TSL:1	n.390-113693C>G		intron	N/A	ENSP00000493727.1
	ZNF385D	ENST00000706131.1		c.326-13349C>G		intron	N/A	ENSP00000516216.1

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9767 AN: 151956 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0315

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0643 AC: 9783 AN: 152074 Hom.: 366 Cov.: 32 AF XY: 0.0624 AC XY: 4636 AN XY: 74334

African (AFR) AF: 0.0613 AC: 2545 AN: 41492

American (AMR) AF: 0.0559 AC: 853 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0315 AC: 109 AN: 3464

East Asian (EAS) AF: 0.126 AC: 653 AN: 5164

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4822

European-Finnish (FIN) AF: 0.0476 AC: 505 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4493 AN: 67968

Other (OTH) AF: 0.0689 AC: 145 AN: 2104

Alfa AF: 0.0281 Hom.: 18

Bravo AF: 0.0648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.41
PhyloP100		-0.90
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: rs9310651; hg19: chr3-21719869;