chr13-32314572-C-T

Variant names:

• chr13-32314572-C-T
• rs206117
• NM_001136571.2:c.-389-22G>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.-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
• 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=-0.89).
• 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 rank	MANE	Protein	UniProt
ZAR1L	NM_001136571.2	c.-389-22G>A		intron_variant	Intron 1 of 5	ENST00000533490.7	NP_001130043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZAR1L	ENST00000533490.7	c.-389-22G>A		intron_variant	Intron 1 of 5	5	NM_001136571.2	ENSP00000437289.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 4 AN: 6

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.451 AC: 46 AN: 102

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.355 AC: 14719 AN: 41518

American (AMR) AF: 0.385 AC: 5889 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2546 AN: 5178

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4820

European-Finnish (FIN) AF: 0.319 AC: 3378 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26135 AN: 67994

Other (OTH) AF: 0.392 AC: 829 AN: 2114

Alfa AF: 0.387 Hom.: 31357

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
PhyloP100		0.45
Mutation Taster		=100/0	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: rs206117; hg19: chr13-32888709;