rs206117

Positions:

• chr13-32314572-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.-389-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,274 control chromosomes in the GnomAD database, including 10,867 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 (10855 hom., cov: 34)
  • Exomes 𝑓: 0.44 (12 hom.)
• Consequence: ZAR1L NM_001136571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZAR1L	NM_001136571.2	c.-389-22G>A		intron_variant		ENST00000533490.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZAR1L	ENST00000533490.7	c.-389-22G>A		intron_variant		5	NM_001136571.2	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56887 AN: 152034 Hom.: 10852 Cov.: 34

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.443 AC: 54 AN: 122 Hom.: 12 Cov.: 0 AF XY: 0.487 AC XY: 39 AN XY: 80

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.667

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.451

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.374 AC: 56922 AN: 152152 Hom.: 10855 Cov.: 34 AF XY: 0.370 AC XY: 27554 AN XY: 74402

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.392

Alfa AF: 0.389 Hom.: 19528

Bravo AF: 0.386

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.84

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: rs206117; hg19: chr13-32888709;