Variant 7-100773854-G-GTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003386.3(ZAN):c.5769_5770insTT(p.Arg1924fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 1,356,342 control chromosomes in the GnomAD database, including 175,140 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.51 ( 12117 hom., cov: 0)

Exomes 𝑓: 0.54 ( 163023 hom. )

Consequence

ZAN
NM_003386.3 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0220

Variant links:

Genes affected

ZAN (HGNC:12857): (zonadhesin) This gene encodes a protein that functions in the species specificity of sperm adhesion to the egg zona pellucida. The encoded protein is located in the acrosome and may be involved in signaling or gamete recognition. An allelic polymorphism in this gene results in both functional and frameshifted alleles; the reference genome represents the functional allele. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2015]

ZAN links:

ZAN (HGNC:):

ZAN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZAN	NM_003386.3 linkuse as main transcript	c.5769_5770insTT	p.Arg1924fs	frameshift_variant	31/48	ENST00000613979.5	NP_003377.2	Q9Y493-1B4DYT6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZAN	ENST00000613979.5 linkuse as main transcript	c.5769_5770insTT	p.Arg1924fs	frameshift_variant	31/48	1	NM_003386.3	ENSP00000480750.1		Q9Y493-1

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

56132

AN:

110574

Hom.:

12123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.492

Gnomad EAS

AF:

0.0508

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.566

Gnomad OTH

AF:

0.532

GnomAD4 exome

AF:

0.538

AC:

669612

AN:

1245732

Hom.:

163023

Cov.:

AF XY:

0.537

AC XY:

332411

AN XY:

618616

show subpopulations

Gnomad4 AFR exome

AF:

0.484

Gnomad4 AMR exome

AF:

0.303

Gnomad4 ASJ exome

AF:

0.481

Gnomad4 EAS exome

AF:

0.0320

Gnomad4 SAS exome

AF:

0.498

Gnomad4 FIN exome

AF:

0.499

Gnomad4 NFE exome

AF:

0.567

Gnomad4 OTH exome

AF:

0.517

GnomAD4 genome

AF:

0.507

AC:

56129

AN:

110610

Hom.:

12117

Cov.:

AF XY:

0.501

AC XY:

27141

AN XY:

54206

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.492

Gnomad4 EAS

AF:

0.0501

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.566

Gnomad4 OTH

AF:

0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over