rs9310679

Positions:

• chr3-22017792-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494118.5(ZNF385D):​c.325+151025C>A variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF385D	XM_011534122.3	c.325+151025C>A		intron_variant			XP_011532424.1
ZNF385D	XM_011534123.3	c.325+151025C>A		intron_variant			XP_011532425.1
ZNF385D	XM_011534124.4	c.325+151025C>A		intron_variant			XP_011532426.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	c.325+151025C>A		intron_variant, NMD_transcript_variant		1		ENSP00000493727
ZNF385D	ENST00000494108.3	c.325+151025C>A		intron_variant		5		ENSP00000495609	P2
ZNF385D	ENST00000706131.1	c.325+151025C>A		intron_variant				ENSP00000516216	A2

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

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.109

Alfa AF: 0.109 Hom.: 520

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310679; hg19: chr3-22059284;