rs206116

Positions:

• chr13-32314346-G-A
• chr13-32314346-G-T

Variant summary

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

The NM_001136571.2(ZAR1L):​c.-185C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,914 control chromosomes in the GnomAD database, including 10,832 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 0.37 (10832 hom., cov: 33)
  • Exomes 𝑓: 0.29 (0 hom.)
• Consequence: ZAR1L NM_001136571.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

ZAR1L (HGNC:37116): (zygote arrest 1 like) This gene encodes a member of the ZAR1 family that is predominantly expressed in oocytes and early embryos. The protein may function as an RNA regulator in early embryos. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZAR1L	NM_001136571.2	c.-185C>T		5_prime_UTR_variant	2/6	ENST00000533490.7	NP_001130043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZAR1L	ENST00000533490.7	c.-185C>T		5_prime_UTR_variant	2/6	5	NM_001136571.2	ENSP00000437289.2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56873 AN: 151782 Hom.: 10829 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.200

GnomAD4 genome AF: 0.375 AC: 56908 AN: 151900 Hom.: 10832 Cov.: 33 AF XY: 0.371 AC XY: 27537 AN XY: 74240

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.392

Alfa AF: 0.368 Hom.: 1282

Bravo AF: 0.387

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs206116; hg19: chr13-32888483;