13-32314336-C-T

Variant names:

• chr13-32314336-C-T
• rs206115
• NM_001136571.2:c.-175G>A

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136571.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZAR1L	NM_001136571.2	MANE Select	c.-175G>A		5_prime_UTR	Exon 2 of 6	NP_001130043.1	A6NP61

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZAR1L	ENST00000533490.7	TSL:5 MANE Select	c.-175G>A		5_prime_UTR	Exon 2 of 6	ENSP00000437289.2	A6NP61

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.504 AC: 20886 AN: 41404

American (AMR) AF: 0.580 AC: 8861 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3309 AN: 5166

South Asian (SAS) AF: 0.481 AC: 2322 AN: 4824

European-Finnish (FIN) AF: 0.568 AC: 5985 AN: 10534

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37964 AN: 67924

Other (OTH) AF: 0.563 AC: 1191 AN: 2114

Alfa AF: 0.556 Hom.: 73633

Bravo AF: 0.555

Asia WGS AF: 0.524 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-1.1
Mutation Taster		=299/1	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: rs206115; hg19: chr13-32888473;