chr13-32314346-G-A

Variant names:

• chr13-32314346-G-A
• rs206116
• NM_001136571.2:c.-185C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZAR1L	NM_001136571.2	MANE Select	c.-185C>T		5_prime_UTR	Exon 2 of 6	NP_001130043.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZAR1L	ENST00000533490.7	TSL:5 MANE Select	c.-185C>T		5_prime_UTR	Exon 2 of 6	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

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: 0.200 AC: 2 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.354 AC: 14662 AN: 41400

American (AMR) AF: 0.385 AC: 5890 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2525 AN: 5166

South Asian (SAS) AF: 0.359 AC: 1733 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3351 AN: 10528

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26215 AN: 67920

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.367 Hom.: 1325

Bravo AF: 0.387

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.078
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs206116; hg19: chr13-32888483;