rs1092913

Variant names:

• chr5-10467590-G-A
• rs1092913
• XM_006714504.4:c.593+6231G>A

Variant summary

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

The ENST00000510520.5(ROPN1L):​n.886-4220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,142 control chromosomes in the GnomAD database, including 4,170 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 0.20 (4170 hom., cov: 33)
• Consequence: ROPN1L ENST00000510520.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 34 publications found

Genes affected

ROPN1L (HGNC:24060): (rhophilin associated tail protein 1 like) This gene encodes a member of the ropporin family. The encoded protein is present in sperm and interacts with A-kinase anchoring protein, AKAP3, through the amphipathic helix region of AKAP3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2014]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510520.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ROPN1L	ENST00000510520.5	TSL:3	n.886-4220G>A		intron	N/A
	ROPN1L	ENST00000718289.1		n.770+6231G>A		intron	N/A
	ROPN1L	ENST00000718290.1		n.699+17477G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29854 AN: 152024 Hom.: 4145 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.197 AC: 29932 AN: 152142 Hom.: 4170 Cov.: 33 AF XY: 0.204 AC XY: 15172 AN XY: 74364

African (AFR) AF: 0.259 AC: 10759 AN: 41468

American (AMR) AF: 0.309 AC: 4729 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3439 AN: 5162

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1190 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7234 AN: 68016

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.156 Hom.: 7190

Bravo AF: 0.217

Asia WGS AF: 0.509 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.27
PhyloP100		-0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1092913;

hg19: chr5-10467702;

COSMIC: COSV56873062;