rs17682132

Positions:

• chr17-9899267-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002903.3(RCVRN):​c.494-1063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,150 control chromosomes in the GnomAD database, including 2,630 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 0.16 (2630 hom., cov: 32)
• Consequence: RCVRN NM_002903.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

RCVRN (HGNC:9937): (recoverin) This gene encodes a member of the recoverin family of neuronal calcium sensors. The encoded protein contains three calcium-binding EF-hand domains and may prolong the termination of the phototransduction cascade in the retina by blocking the phosphorylation of photo-activated rhodopsin. Recoverin may be the antigen responsible for cancer-associated retinopathy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RCVRN	NM_002903.3	c.494-1063C>T		intron_variant		ENST00000226193.6	NP_002894.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RCVRN	ENST00000226193.6	c.494-1063C>T		intron_variant		1	NM_002903.3	ENSP00000226193	P1
RCVRN	ENST00000570909.3	n.215-1063C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24831 AN: 152032 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.163 AC: 24824 AN: 152150 Hom.: 2630 Cov.: 32 AF XY: 0.162 AC XY: 12057 AN XY: 74376

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0439

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.155

Alfa AF: 0.222 Hom.: 8075

Bravo AF: 0.150

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.3
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs17682132; hg19: chr17-9802584;