Variant 5-138441137-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001271803.2(REEP2):c.105+49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00979 in 1,610,122 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0072 ( 15 hom., cov: 33)

Exomes 𝑓: 0.010 ( 82 hom. )

Consequence

REEP2
NM_001271803.2 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.697

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 5-138441137-G-A is Benign according to our data. Variant chr5-138441137-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00718 (1094/152352) while in subpopulation NFE AF= 0.0116 (788/68036). AF 95% confidence interval is 0.0109. There are 15 homozygotes in gnomad4. There are 517 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
REEP2	NM_001271803.2 linkuse as main transcript	c.105+49G>A	intron_variant	ENST00000378339.7	NP_001258732.1
REEP2	NM_016606.4 linkuse as main transcript	c.105+49G>A	intron_variant		NP_057690.2
REEP2	NR_073448.2 linkuse as main transcript	n.332+49G>A	intron_variant, non_coding_transcript_variant
REEP2	NR_073449.2 linkuse as main transcript	n.332+49G>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REEP2	ENST00000378339.7 linkuse as main transcript	c.105+49G>A		intron_variant		1	NM_001271803.2	ENSP00000367590	A1	Q9BRK0-2

Frequencies

GnomAD3 genomes

AF:

0.00719

AC:

1094

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00166

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00595

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0105

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00664

AC:

1620

AN:

244130

Hom.:

AF XY:

0.00679

AC XY:

897

AN XY:

132128

show subpopulations

Gnomad AFR exome

AF:

0.00176

Gnomad AMR exome

AF:

0.00414

Gnomad ASJ exome

AF:

0.000506

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00211

Gnomad FIN exome

AF:

0.00962

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00864

GnomAD4 exome

AF:

0.0101

AC:

14677

AN:

1457770

Hom.:

Cov.:

AF XY:

0.00986

AC XY:

7150

AN XY:

725264

show subpopulations

Gnomad4 AFR exome

AF:

0.00183

Gnomad4 AMR exome

AF:

0.00460

Gnomad4 ASJ exome

AF:

0.000575

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00223

Gnomad4 FIN exome

AF:

0.0111

Gnomad4 NFE exome

AF:

0.0118

Gnomad4 OTH exome

AF:

0.00779

GnomAD4 genome

AF:

0.00718

AC:

1094

AN:

152352

Hom.:

Cov.:

AF XY:

0.00694

AC XY:

517

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00595

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.0105

Gnomad4 NFE

AF:

0.0116

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00764

Hom.:

Bravo

AF:

0.00659

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 24, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.4

DANN

Benign

0.71

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