chr5-112907271-C-T

Variant names:

• chr5-112907271-C-T
• rs469727
• NM_005669.5:c.213-4753G>A

Variant summary

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

The NM_005669.5(REEP5):​c.213-4753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,986 control chromosomes in the GnomAD database, including 10,829 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 0.37 (10829 hom., cov: 32)
• Consequence: REEP5 NM_005669.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 26 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005669.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REEP5	NM_005669.5	MANE Select	c.213-4753G>A		intron	N/A	NP_005660.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REEP5	ENST00000379638.9	TSL:1 MANE Select	c.213-4753G>A		intron	N/A	ENSP00000368959.4
	REEP5	ENST00000497856.6	TSL:1	n.353-4753G>A		intron	N/A
	REEP5	ENST00000261482.8	TSL:5	c.186-4753G>A		intron	N/A	ENSP00000261482.4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56188 AN: 151868 Hom.: 10804 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.370 AC: 56276 AN: 151986 Hom.: 10829 Cov.: 32 AF XY: 0.367 AC XY: 27258 AN XY: 74292

African (AFR) AF: 0.473 AC: 19582 AN: 41436

American (AMR) AF: 0.317 AC: 4839 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3468

East Asian (EAS) AF: 0.166 AC: 862 AN: 5182

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4814

European-Finnish (FIN) AF: 0.371 AC: 3911 AN: 10550

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23338 AN: 67952

Other (OTH) AF: 0.359 AC: 754 AN: 2102

Alfa AF: 0.345 Hom.: 30253

Bravo AF: 0.368

Asia WGS AF: 0.233 AC: 815 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	7.8
DANN	Benign	0.70
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs469727; hg19: chr5-112242968; COSMIC: COSV54841188;