9-27290727-A-C

Position:

• chr9-27290727-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020641.3(EQTN):​c.421+292T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,152 control chromosomes in the GnomAD database, including 21,372 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 0.51 (21372 hom., cov: 34)
• Consequence: EQTN NM_020641.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752

Genes affected

EQTN (HGNC:1359): (equatorin) Predicted to be involved in acrosomal vesicle exocytosis; endocytosis; and fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in acrosomal membrane; early endosome; and nucleus. Predicted to be active in inner acrosomal membrane; outer acrosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EQTN	NM_020641.3	c.421+292T>G		intron_variant		ENST00000380032.8	NP_065692.2
EQTN	NM_001161585.2	c.334+292T>G		intron_variant			NP_001155057.1
EQTN	XM_011517920.2	c.13+292T>G		intron_variant			XP_011516222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EQTN	ENST00000380032.8	c.421+292T>G		intron_variant		1	NM_020641.3	ENSP00000369371	P1
EQTN	ENST00000537675.5	c.334+292T>G		intron_variant		1		ENSP00000441630

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78002 AN: 152034 Hom.: 21358 Cov.: 34

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.513 AC: 78048 AN: 152152 Hom.: 21372 Cov.: 34 AF XY: 0.512 AC XY: 38103 AN XY: 74374

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.548

Alfa AF: 0.587 Hom.: 13923

Bravo AF: 0.501

Asia WGS AF: 0.528 AC: 1832 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.68

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: rs911602; hg19: chr9-27290725;