5-138440751-G-A

Position:

• chr5-138440751-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001271803.2(REEP2):​c.33-265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 152,290 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.027 (80 hom., cov: 33)
• Consequence: REEP2 NM_001271803.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.152

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=-0.83).
• BP6: Variant 5-138440751-G-A is Benign according to our data. Variant chr5-138440751-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1329742.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0271 (4121/152290) while in subpopulation NFE AF= 0.0357 (2425/68006). AF 95% confidence interval is 0.0345. There are 80 homozygotes in gnomad4. There are 1942 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 80 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REEP2	NM_001271803.2	c.33-265G>A		intron_variant		ENST00000378339.7
REEP2	NM_016606.4	c.33-265G>A		intron_variant
REEP2	NR_073448.2	n.185-190G>A		intron_variant, non_coding_transcript_variant
REEP2	NR_073449.2	n.185-190G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REEP2	ENST00000378339.7	c.33-265G>A		intron_variant		1	NM_001271803.2	A1

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4112 AN: 152172 Hom.: 80 Cov.: 33

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0271 AC: 4121 AN: 152290 Hom.: 80 Cov.: 33 AF XY: 0.0261 AC XY: 1942 AN XY: 74450

Gnomad4 AFR AF: 0.0220

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0321 Hom.: 13

Bravo AF: 0.0260

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs111848060; hg19: chr5-137776440;