rs2412779

Variant names:

• chr15-43363729-A-G
• rs2412779
• NM_001372080.1:c.1690+186T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZSCAN29	NM_001372080.1	c.1690+186T>C		intron_variant	Intron 5 of 5	ENST00000684362.1	NP_001359009.1
ZSCAN29	NM_152455.4	c.1690+186T>C		intron_variant	Intron 4 of 4		NP_689668.3
ZSCAN29	XM_047432187.1	c.1690+186T>C		intron_variant	Intron 5 of 5		XP_047288143.1
ZSCAN29	XM_047432188.1	c.712+186T>C		intron_variant	Intron 3 of 3		XP_047288144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN29	ENST00000684362.1	c.1690+186T>C		intron_variant	Intron 5 of 5		NM_001372080.1	ENSP00000507363.1

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

African (AFR) AF: 0.634 AC: 7646 AN: 12058

American (AMR) AF: 0.203 AC: 3096 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 2493 AN: 12666

East Asian (EAS) AF: 0.472 AC: 14065 AN: 29814

South Asian (SAS) AF: 0.222 AC: 6423 AN: 28910

European-Finnish (FIN) AF: 0.0836 AC: 2286 AN: 27352

Middle Eastern (MID) AF: 0.166 AC: 304 AN: 1832

European-Non Finnish (NFE) AF: 0.110 AC: 27788 AN: 252660

Other (OTH) AF: 0.189 AC: 4540 AN: 24014

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

African (AFR) AF: 0.625 AC: 25916 AN: 41434

American (AMR) AF: 0.211 AC: 3229 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5160

South Asian (SAS) AF: 0.238 AC: 1150 AN: 4822

European-Finnish (FIN) AF: 0.0869 AC: 922 AN: 10604

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7412 AN: 67986

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.171 Hom.: 4874

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
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2412779; hg19: chr15-43655927;