rs6594652

chr5-112911429-T-A

Variant summary

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

The NM_005669.5(REEP5):c.213-8911A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,288 control chromosomes in the GnomAD database, including 519 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 0.052 (519 hom., cov: 32)
• Consequence: REEP5 NM_005669.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

Genes affected

REEP5 (HGNC:30077): (receptor accessory protein 5) Predicted to be involved in endoplasmic reticulum organization and regulation of intracellular transport. Located in endoplasmic reticulum tubular network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REEP5	NM_005669.5	c.213-8911A>T		intron_variant		ENST00000379638.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REEP5	ENST00000379638.9	c.213-8911A>T		intron_variant		1	NM_005669.5	P1

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7969 AN: 152170 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.000941

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00416

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0524 AC: 7977 AN: 152288 Hom.: 519 Cov.: 32 AF XY: 0.0533 AC XY: 3970 AN XY: 74480

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.000941

Gnomad4 NFE AF: 0.00416

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0302 Hom.: 32

Bravo AF: 0.0617

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	16
Dann	Benign	0.95

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: rs6594652; hg19: chr5-112247126;