13-32314214-ATTAGAC-A

Position:

• chr13-32314214-ATTAGAC-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001136571.2(ZAR1L):​c.-169+110_-169+115del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,710 control chromosomes in the GnomAD database, including 11,018 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (11018 hom., cov: 0)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ZAR1L NM_001136571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZAR1L	NM_001136571.2	c.-169+110_-169+115del		intron_variant		ENST00000533490.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZAR1L	ENST00000533490.7	c.-169+110_-169+115del		intron_variant		5	NM_001136571.2	P1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57423 AN: 151588 Hom.: 11014 Cov.: 0

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.379 AC: 57461 AN: 151708 Hom.: 11018 Cov.: 0 AF XY: 0.375 AC XY: 27790 AN XY: 74178

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.396

Alfa AF: 0.372 Hom.: 1263

Bravo AF: 0.393

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3072036; hg19: chr13-32888351;