rs10513650

Variant names:

• chr3-21804132-T-C
• rs10513650
• ENST00000494118.5:n.389+45524A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-21804132-T-C
• chr3-21804132-T-G

Variant summary

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

The ENST00000706131.1(ZNF385D):​c.326-139104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 152,304 control chromosomes in the GnomAD database, including 582 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 0.057 (582 hom., cov: 33)
• Consequence: ZNF385D ENST00000706131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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.389+45524A>G		intron	N/A	ENSP00000493727.1	A0A2R8Y4E5
	ZNF385D	ENST00000706131.1		c.326-139104A>G		intron	N/A	ENSP00000516216.1	A0A994J5P6
	ZNF385D	ENST00000494108.3	TSL:5	c.326-139104A>G		intron	N/A	ENSP00000495609.3	A0A2R8YG37

Frequencies

GnomAD3 genomes AF: 0.0571 AC: 8684 AN: 152184 Hom.: 578 Cov.: 33

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0570 AC: 8688 AN: 152304 Hom.: 582 Cov.: 33 AF XY: 0.0628 AC XY: 4679 AN XY: 74472

African (AFR) AF: 0.0163 AC: 676 AN: 41574

American (AMR) AF: 0.136 AC: 2080 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1577 AN: 5180

South Asian (SAS) AF: 0.120 AC: 579 AN: 4828

European-Finnish (FIN) AF: 0.0602 AC: 639 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2843 AN: 68024

Other (OTH) AF: 0.0591 AC: 125 AN: 2114

Alfa AF: 0.0163 Hom.: 8

Bravo AF: 0.0597

Asia WGS AF: 0.183 AC: 635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.68
PhyloP100		-0.58

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: rs10513650;

hg19: chr3-21845624;