rs2412779

Positions:

• chr15-43363729-A-G

Variant summary

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

The NM_001372080.1(ZSCAN29):​c.1690+186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 556,620 control chromosomes in the GnomAD database, including 19,134 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 0.28 (9722 hom., cov: 31)
  • Exomes 𝑓: 0.17 (9412 hom.)
• Consequence: ZSCAN29 NM_001372080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

ZSCAN29 (HGNC:26673): (zinc finger and SCAN domain containing 29) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN29	NM_001372080.1	c.1690+186T>C		intron_variant		ENST00000684362.1	NP_001359009.1
ZSCAN29	NM_152455.4	c.1690+186T>C		intron_variant			NP_689668.3
ZSCAN29	XM_047432187.1	c.1690+186T>C		intron_variant			XP_047288143.1
ZSCAN29	XM_047432188.1	c.712+186T>C		intron_variant			XP_047288144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN29	ENST00000684362.1	c.1690+186T>C		intron_variant			NM_001372080.1	ENSP00000507363	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42221 AN: 151944 Hom.: 9687 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.170 AC: 68641 AN: 404558 Hom.: 9412 Cov.: 5 AF XY: 0.169 AC XY: 35195 AN XY: 208618

Gnomad4 AFR exome AF: 0.634

Gnomad4 AMR exome AF: 0.203

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.472

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.0836

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.278 AC: 42314 AN: 152062 Hom.: 9722 Cov.: 31 AF XY: 0.275 AC XY: 20437 AN XY: 74344

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.237

Alfa AF: 0.150 Hom.: 2648

Bravo AF: 0.307

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.37

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: rs2412779; hg19: chr15-43655927;