rs206143

Variant names:

• chr13-32306489-G-A
• rs206143
• NM_001136571.2:c.822+2197C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-32306489-G-A
• chr13-32306489-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136571.2(ZAR1L):​c.822+2197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,980 control chromosomes in the GnomAD database, including 10,720 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 (10720 hom., cov: 32)
• Consequence: ZAR1L NM_001136571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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.822+2197C>T		intron	N/A	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.822+2197C>T		intron	N/A	ENSP00000437289.2	A6NP61
	ZAR1L	ENST00000345108.6	TSL:1	c.822+2197C>T		intron	N/A	ENSP00000344616.5	A6NP61

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56566 AN: 151858 Hom.: 10717 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.389

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.372 AC: 56601 AN: 151980 Hom.: 10720 Cov.: 32 AF XY: 0.369 AC XY: 27411 AN XY: 74260

African (AFR) AF: 0.353 AC: 14633 AN: 41448

American (AMR) AF: 0.382 AC: 5846 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2538 AN: 5170

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3453 AN: 10548

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25997 AN: 67936

Other (OTH) AF: 0.386 AC: 813 AN: 2104

Alfa AF: 0.375 Hom.: 1799

Bravo AF: 0.384

Asia WGS AF: 0.363 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.58
PhyloP100		0.34
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: rs206143; hg19: chr13-32880626;