5-138441242-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001271803.2(REEP2):c.106-143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 1,256,162 control chromosomes in the GnomAD database, including 95,691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8561 hom., cov: 32)
  • Exomes 𝑓: 0.39 (87130 hom.)
• Consequence: REEP2 NM_001271803.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.464

Genes affected

REEP2 (HGNC:17975): (receptor accessory protein 2) This gene encodes a member of the receptor expression enhancing protein family. Studies of a related gene in mouse suggest that the encoded protein is found in the cell membrane and enhances the function of sweet taste receptors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 5-138441242-C-T is Benign according to our data. Variant chr5-138441242-C-T is described in ClinVar as [Benign]. Clinvar id is 1295465.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REEP2	NM_001271803.2	c.106-143C>T		intron_variant		ENST00000378339.7
REEP2	NM_016606.4	c.106-143C>T		intron_variant
REEP2	NR_073448.2	n.333-143C>T		intron_variant, non_coding_transcript_variant
REEP2	NR_073449.2	n.333-143C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REEP2	ENST00000378339.7	c.106-143C>T		intron_variant		1	NM_001271803.2	A1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48789 AN: 151952 Hom.: 8550 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.389 AC: 429094 AN: 1104092 Hom.: 87130 Cov.: 15 AF XY: 0.396 AC XY: 221832 AN XY: 560612

Gnomad4 AFR exome AF: 0.198

Gnomad4 AMR exome AF: 0.213

Gnomad4 ASJ exome AF: 0.332

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.549

Gnomad4 FIN exome AF: 0.334

Gnomad4 NFE exome AF: 0.401

Gnomad4 OTH exome AF: 0.363

GnomAD4 genome AF: 0.321 AC: 48818 AN: 152070 Hom.: 8561 Cov.: 32 AF XY: 0.319 AC XY: 23702 AN XY: 74348

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.303

Alfa AF: 0.369 Hom.: 10182

Bravo AF: 0.304

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 24, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.28

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: rs2269947; hg19: chr5-137776931;