rs957589

Variant names:

• chr3-21710558-G-A
• rs957589
• NM_024697.3:c.22+40337C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-21710558-G-A
• chr3-21710558-G-C

Variant summary

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

The NM_024697.3(ZNF385D):​c.22+40337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,916 control chromosomes in the GnomAD database, including 17,409 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 0.47 (17409 hom., cov: 32)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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 = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3	c.22+40337C>T		intron_variant	Intron 1 of 7	ENST00000281523.8	NP_078973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000281523.8	c.22+40337C>T		intron_variant	Intron 1 of 7	1	NM_024697.3	ENSP00000281523.2

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70881 AN: 151798 Hom.: 17378 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.467 AC: 70961 AN: 151916 Hom.: 17409 Cov.: 32 AF XY: 0.469 AC XY: 34846 AN XY: 74226

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.448

Alfa AF: 0.407 Hom.: 26076

Bravo AF: 0.463

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs957589; hg19: chr3-21752050;