rs814597

Variant names:

• chr5-10468817-C-T
• rs814597
• ENST00000510520.5:n.886-2993C>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ROPN1L	XM_006714504.4	c.593+7458C>T		intron_variant	Intron 5 of 6		XP_006714567.1
ROPN1L	XM_017009946.3	c.594-2993C>T		intron_variant	Intron 5 of 5		XP_016865435.1
ROPN1L	XM_047417808.1	c.594-2993C>T		intron_variant	Intron 4 of 4		XP_047273764.1
ROPN1L	XM_017009947.3	c.593+7458C>T		intron_variant	Intron 5 of 6		XP_016865436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ROPN1L	ENST00000510520.5	n.886-2993C>T		intron_variant	Intron 4 of 4	3
ROPN1L	ENST00000718289.1	n.770+7458C>T		intron_variant	Intron 5 of 6
ROPN1L	ENST00000718290.1	n.699+18704C>T		intron_variant	Intron 3 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs814597; hg19: chr5-10468929;