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 ENST00000494118.5(ZNF385D):​n.389+45524A>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 ENST00000494118.5 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.326-139104A>G		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.326-139104A>G		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_017007193.2	c.112+45524A>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+45524A>G		intron_variant	Intron 3 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.326-139104A>G		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.326-139104A>G		intron_variant	Intron 3 of 9	5		ENSP00000495609.3

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 v4.3

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

Other links and lift over

dbSNP: rs10513650; hg19: chr3-21845624;