rs13077624

Variant names:

• chr3-21721118-G-A
• rs13077624
• NM_024697.3:c.22+29777C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-21721118-G-A
• chr3-21721118-G-C
• chr3-21721118-G-T

Variant summary

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

The NM_024697.3(ZNF385D):​c.22+29777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,334 control chromosomes in the GnomAD database, including 2,539 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 0.17 (2539 hom., cov: 31)
• Consequence: ZNF385D NM_024697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	NM_024697.3	c.22+29777C>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+29777C>T		intron_variant	Intron 1 of 7	1	NM_024697.3	ENSP00000281523.2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25253 AN: 151216 Hom.: 2534 Cov.: 31

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.167 AC: 25272 AN: 151334 Hom.: 2539 Cov.: 31 AF XY: 0.168 AC XY: 12403 AN XY: 73906

Gnomad4 AFR AF: 0.0690

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.195

Alfa AF: 0.136 Hom.: 335

Bravo AF: 0.176

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.75

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: rs13077624; hg19: chr3-21762610;