chr3-123986995-G-A

Variant names:

• chr3-123986995-G-A
• rs4499545
• NM_001317774.2:c.-13+4927C>T

Variant summary

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

The NM_017578.5(ROPN1):​c.-170+4186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,218 control chromosomes in the GnomAD database, including 2,431 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 0.18 (2431 hom., cov: 33)
• Consequence: ROPN1 NM_017578.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 4 publications found

Genes affected

ROPN1 (HGNC:17692): (rhophilin associated tail protein 1) The protein encoded by this gene is found in the fibrous sheath of spermatazoa, where it interacts with rhophilin, a Rho GTPase binding protein. The encoded protein also can bind an A-kinase anchoring protein (AKAP110) and a calcium-binding tyrosine phosphorylation-regulated protein (CABYR). This protein may be involved in sperm motility and has been shown to be a cancer-testis antigen in hematologic malignancies. Several transcript variants, some protein-coding and some non-protein coding, have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017578.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROPN1	NM_001317774.2	MANE Select	c.-13+4927C>T		intron	N/A	NP_001304703.1
	ROPN1	NM_001394217.1		c.-59+4927C>T		intron	N/A	NP_001381146.1
	ROPN1	NM_001394218.1		c.-170+4927C>T		intron	N/A	NP_001381147.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROPN1	ENST00000405845.8	TSL:1 MANE Select	c.-13+4927C>T		intron	N/A	ENSP00000385919.3
	ROPN1	ENST00000184183.8	TSL:1	c.-170+4186C>T		intron	N/A	ENSP00000184183.4
	ROPN1	ENST00000459660.5	TSL:1	c.-59+5049C>T		intron	N/A	ENSP00000420590.1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27163 AN: 152098 Hom.: 2431 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.179 AC: 27185 AN: 152218 Hom.: 2431 Cov.: 33 AF XY: 0.179 AC XY: 13342 AN XY: 74414

African (AFR) AF: 0.195 AC: 8112 AN: 41562

American (AMR) AF: 0.149 AC: 2282 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3472

East Asian (EAS) AF: 0.0836 AC: 432 AN: 5166

South Asian (SAS) AF: 0.162 AC: 782 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2070 AN: 10606

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12350 AN: 67986

Other (OTH) AF: 0.189 AC: 400 AN: 2116

Alfa AF: 0.134 Hom.: 525

Bravo AF: 0.176

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.89
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: rs4499545; hg19: chr3-123705842;