rs9310679

Variant names:

• chr3-22017792-G-T
• rs9310679
• ENST00000494118.5:n.325+151025C>A

Variant summary

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

The ENST00000494118.5(ZNF385D):​n.325+151025C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,672 control chromosomes in the GnomAD database, including 1,201 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 0.12 (1201 hom., cov: 33)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.325+151025C>A		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.325+151025C>A		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_047448956.1	c.9+151025C>A		intron_variant	Intron 1 of 9		XP_047304912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.325+151025C>A		intron_variant	Intron 2 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.325+151025C>A		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.325+151025C>A		intron_variant	Intron 3 of 9	5		ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18049 AN: 151554 Hom.: 1201 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.119 AC: 18081 AN: 151672 Hom.: 1201 Cov.: 33 AF XY: 0.119 AC XY: 8822 AN XY: 74106

African (AFR) AF: 0.164 AC: 6782 AN: 41398

American (AMR) AF: 0.109 AC: 1666 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 442 AN: 3464

East Asian (EAS) AF: 0.0705 AC: 363 AN: 5152

South Asian (SAS) AF: 0.134 AC: 645 AN: 4816

European-Finnish (FIN) AF: 0.106 AC: 1113 AN: 10506

Middle Eastern (MID) AF: 0.179 AC: 52 AN: 290

European-Non Finnish (NFE) AF: 0.0975 AC: 6613 AN: 67814

Other (OTH) AF: 0.109 AC: 229 AN: 2106

Alfa AF: 0.111 Hom.: 607

Bravo AF: 0.121

Asia WGS AF: 0.0950 AC: 326 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9310679; hg19: chr3-22059284;