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. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZAR1L	NM_001136571.2	c.822+2197C>T		intron_variant	Intron 5 of 5	ENST00000533490.7	NP_001130043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZAR1L	ENST00000533490.7	c.822+2197C>T		intron_variant	Intron 5 of 5	5	NM_001136571.2	ENSP00000437289.2
ZAR1L	ENST00000345108.6	c.822+2197C>T		intron_variant	Intron 3 of 3	1		ENSP00000344616.5

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.386

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs206143; hg19: chr13-32880626;