5-138439392-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_001271803.2(REEP2):c.32+152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 729,952 control chromosomes in the GnomAD database, including 19,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.24 (4831 hom., cov: 31)
  • Exomes 𝑓: 0.20 (14288 hom.)
• Consequence: REEP2 NM_001271803.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.25

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP6: Variant 5-138439392-C-T is Benign according to our data. Variant chr5-138439392-C-T is described in ClinVar as [Benign]. Clinvar id is 1235420.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REEP2	NM_001271803.2	c.32+152C>T		intron_variant		ENST00000378339.7
REEP2	NM_016606.4	c.32+152C>T		intron_variant
REEP2	NR_073448.2	n.184+152C>T		intron_variant, non_coding_transcript_variant
REEP2	NR_073449.2	n.184+152C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REEP2	ENST00000378339.7	c.32+152C>T		intron_variant		1	NM_001271803.2	A1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36322 AN: 151822 Hom.: 4825 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.200 AC: 115499 AN: 578012 Hom.: 14288 AF XY: 0.198 AC XY: 60045 AN XY: 302978

Gnomad4 AFR exome AF: 0.281

Gnomad4 AMR exome AF: 0.264

Gnomad4 ASJ exome AF: 0.289

Gnomad4 EAS exome AF: 0.506

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.206

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.222

GnomAD4 genome AF: 0.239 AC: 36337 AN: 151940 Hom.: 4831 Cov.: 31 AF XY: 0.243 AC XY: 18080 AN XY: 74270

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.256

Alfa AF: 0.143 Hom.: 370

Bravo AF: 0.251

Asia WGS AF: 0.340 AC: 1182 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	-0.44
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: rs1859466; hg19: chr5-137775081; COSMIC: COSV54734731; COSMIC: COSV54734731;