5-10468817-C-T

Variant names:

• chr5-10468817-C-T
• rs814597
• XM_006714504.4:c.593+7458C>T

Variant summary

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

The ENST00000510520.5(ROPN1L):​n.886-2993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,082 control chromosomes in the GnomAD database, including 3,712 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 (3712 hom., cov: 33)
• Consequence: ROPN1L ENST00000510520.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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.886-2993C>T		intron	N/A
	ROPN1L	ENST00000718289.1		n.770+7458C>T		intron	N/A
	ROPN1L	ENST00000718290.1		n.699+18704C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27708 AN: 151966 Hom.: 3687 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.183 AC: 27771 AN: 152082 Hom.: 3712 Cov.: 33 AF XY: 0.190 AC XY: 14153 AN XY: 74330

African (AFR) AF: 0.211 AC: 8739 AN: 41468

American (AMR) AF: 0.302 AC: 4608 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3459 AN: 5148

South Asian (SAS) AF: 0.311 AC: 1496 AN: 4812

European-Finnish (FIN) AF: 0.113 AC: 1192 AN: 10572

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7215 AN: 68016

Other (OTH) AF: 0.180 AC: 380 AN: 2114

Alfa AF: 0.136 Hom.: 1151

Bravo AF: 0.200

Asia WGS AF: 0.504 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.67
PhyloP100		-0.050

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: rs814597;

hg19: chr5-10468929;