13-32314336-C-T

Position:

• chr13-32314336-C-T

Variant summary

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

The NM_001136571.2(ZAR1L):​c.-175G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,936 control chromosomes in the GnomAD database, including 22,880 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 0.55 (22879 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ZAR1L NM_001136571.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZAR1L	NM_001136571.2	c.-175G>A		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.-175G>A		5_prime_UTR_variant	2/6	5	NM_001136571.2	ENSP00000437289.2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82819 AN: 151806 Hom.: 22865 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.566

GnomAD4 exome AF: 0.500 AC: 6 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 5 AN XY: 10

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.546 AC: 82883 AN: 151924 Hom.: 22879 Cov.: 33 AF XY: 0.544 AC XY: 40426 AN XY: 74262

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.563

Alfa AF: 0.556 Hom.: 25209

Bravo AF: 0.555

Asia WGS AF: 0.524 AC: 1819 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	1.1
DANN	Benign	0.63

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: rs206115; hg19: chr13-32888473;