chr9-27290727-A-C

Variant names:

• chr9-27290727-A-C
• rs911602
• NM_020641.3:c.421+292T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020641.3. 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
	EQTN	NM_020641.3	MANE Select	c.421+292T>G		intron	N/A	NP_065692.2	Q9NQ60-1
	EQTN	NM_001161585.2		c.334+292T>G		intron	N/A	NP_001155057.1	Q9NQ60-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EQTN	ENST00000380032.8	TSL:1 MANE Select	c.421+292T>G		intron	N/A	ENSP00000369371.3	Q9NQ60-1
	EQTN	ENST00000537675.5	TSL:1	c.334+292T>G		intron	N/A	ENSP00000441630.1	Q9NQ60-3

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

African (AFR) AF: 0.312 AC: 12938 AN: 41512

American (AMR) AF: 0.522 AC: 7977 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2530 AN: 5176

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4820

European-Finnish (FIN) AF: 0.555 AC: 5876 AN: 10580

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41816 AN: 67982

Other (OTH) AF: 0.548 AC: 1160 AN: 2116

Alfa AF: 0.588 Hom.: 15331

Bravo AF: 0.501

Asia WGS AF: 0.528 AC: 1832 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.68
PhyloP100		0.75
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: rs911602; hg19: chr9-27290725;