Variant 5-138441242-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.464

Variant links:

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]

REEP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	MANE	Protein	UniProt
REEP2	NM_001271803.2 link	c.106-143C>T	intron_variant	ENST00000378339.7	NP_001258732.1	Q9BRK0-2A8K3D2
REEP2	NM_016606.4 link	c.106-143C>T	intron_variant		NP_057690.2	Q9BRK0-1A8K3D2
REEP2	NR_073448.2 link	n.333-143C>T	intron_variant
REEP2	NR_073449.2 link	n.333-143C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REEP2	ENST00000378339.7 link	c.106-143C>T		intron_variant		1	NM_001271803.2	ENSP00000367590.2		Q9BRK0-2

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48789

AN:

151952

Hom.:

8550

Cov.:

show subpopulations

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.:

AF XY:

0.396

AC XY:

221832

AN XY:

560612

show subpopulations

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.:

AF XY:

0.319

AC XY:

23702

AN XY:

74348

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 24, 2021

- -

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over